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7/2017 Jason Wallace
Canas, RA, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.16.00613
   Exploiting the genetic diversity of maize using a combined metabolomic, enzyme activity profiling, and metabolic modelling approach to link leaf physiology to kernel yield

The authors used a panel of 19 European and American maize lines to investigate patterns among metabolites, enzyme activity, and metabolic flux. Leaf metabolites and enzyme activities were assayed during vegetative (7-8 leaf stage) and grain-filling (15 days after silking) growth. The authors performed clustering of lines based on different metabolic or enzymatic measures, and also performed metabolic modeling and cluster analysis to identify differences among lines and which of these differences may influence yield. The authors find many correlations among traits, although with only 19 lines it is questionable how many of them would replicate across a larger panel. Ultimately, this paper provides some very interesting descriptive analysis of metabolism in diverse maize lines, though it remains to be seen how useful the derived predictions will be. Jason Wallace, 2017

7/2017 Fang Bai
Jiao, YP, et al. 2017. Nature. 0:10.1038/nature22971
   Improved maize reference genome with single-molecule technologies

This paper announces Zm-B73-REFERENCE-GRAMENE-4.0, also known as B73 RefGen_v4, AGPv4. The annotation set is called Zm0001d. This paper was officially published June 12, 2017. From this date the sequence is no longer under the Toronto agreement.

Due to the large and complex identity, it is always a challenge to assemble the maize genome accurately. The old version of maize genome was assembled by using the Sanger Sequencing which was composed of more than 100,000 small contigs and missed some complex repeat regions. In this paper, the new version of maize genome was assembled by Jiao et al. based on a 65x Single-Molecule Real-Time Sequencing (SMRT) and high-resolution optical mapping. This version of B73 genome is composed of 2,958 contigs, which significantly increase the contig length and notably reduce the assemble errors. Fang Bai 2017

7/2017 Lin Li
Gent, JI; Wang, N; Dawe, RK. 2017. Genome Biol. 18:121
   Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives

Centromeres, the gene desert, seem mysterious to many scientists given its ultra-complex composition and structure. In this paper, the authors have conducted a comparative genomic analysis based on CenH3 ChIP-Seq data maize and its wild relatives Z. mays parviglumis, Z. mays mexicana, and Z. mays huehuetenangensis, defined the complex centromeres, and revealed the stability of centromere positioning. The study provides us evidence to reject the hypothesis that complex centromeres are an outcome of cultivation and inbreeding, furthers our understanding of centromeres at a population level. Lin Li, 2017

6/2017 Jason Wallace
Lorant, A et al. 2017. bioRxiv preprint 0:doi: 10.1101/105940
   The Potential Role of Genetic Assimilation during Maize Domestication

Most studies of crop domestication compare existing crops to their existing wild relatives, since archaeological remains and ancient DNA are both extremely rare. To investigate the process of maize domestication, Lorant et al. grew maize and teosinte under environmental conditions similar to those expected to be present at the time of maize domestication. Under these conditions, teosinte exhibits several maize-like traits, and the authors propose that during domestication these traits became genetically fixed (a process called "genetic assimilation"). They performed transcriptome analysis of maize and teosinte under both ancient and modern climactic conditions and found ~2000 genes that altered expression in teosinte but showed no such change in maize. These results imply that these genes are no longer environmentally responsive but instead are genetically fixed, at least under the conditions tested. Although some of these genes coincide with previously identified selective sweeps, as a group they are not enriched for domestication loci, so other processes may also have been at work. Jason Wallace, 2017

This paper discovers several thousand differentially expressed genes between teosinte and maize in an environment similar to the time of early domestication (Early Holocene). Some genes were differentially expressed only in teosinte, suggesting genetic assimilation may have occured. They include the following auxin and auxin response genes:SAUR33 (GRMZM2G460861), auxin efflux carrier PIN5a (GRMZM2G025742), AUX IAA (GRMZM2G057067) and a PAR (GRMZM2G423863). Also with evidence of assimilation were TCP (TEOSINTEBRANCHED1/ CYCLOIDEA/PCF) transcription factor 44 (GRMZM2G089361), ZOG3 (GRMZM2G338465), gibberellin and ABA regulators GRMZM2G301932 and GRMZM2G338465, and nitrate reductase NADH1 (GRMZM2G568636) and ferredoxin1 (GRMZM2G043162). These are the only gene models mentioned in the paper.

These USDA teosinte accessions were used in this study: PI 384062, PI 384063, PI 384071, PI 566692

These USDA maize accessions were used in this study: Ames 19288 Oh43, PI 550473 B73, NSL 30053 W22, PI 558532 Mo17

6/2017 Fang Bai
Yang, Y-Z, et al. 2017. Plant Physiol. 0:doi: 10.1104/pp.16.01295
   Small kernel2 encodes a glutaminase in vitamin B6 biosynthesis essential for maize seed development

Vitamin B6 is one of the essential nutrients and its active form of pyridoxal 5'-phosphate is a coenzyme involved in several aspects of metabolisms. Recent study showed that Vitamin B6 plays the role in the embryo development in Arabidopsis. In this paper, Yang et al. study the roles of vitamin B6 in embryogenesis and endosperm development in maize. They identified a recessive embryo-lethal mutant small kernel2-1 (smk2-1) from the UniformMu transposon mutagenesis population and cloned smk2 by transposon tagging and sequencing. Yang et al. found that smk2 is a vitamin B6 biosynthetic mutant of maize. The homozygote mutants affected the embryogenesis in maize which is the same as in Arabidopsis, but had fewer effects in endosperm development. smk2 encodes the glutaminase subunit of the PLP synthase. The subcellular localization results showed that SMK2 is located in the cytosol. The authors measured the vitamin B6 contents in the embryo and endosperm of the mutants and their wild type (WT) sibling seeds by HPLC and found that the content of total vitamin B6 was drastically reduced in both embryo and endosperm of mutants compared to the WT. Also, based on the evidences that the maize smk2 partially complements the Arabidopsis pdx2.1 and the yeast MML21 mutant phenotypes, as well as the application of the vitamin B6 partially rescued the smk2 mutant, they concluded that SMK2 functions in vitamin B6 biosynthesis in maize. Fang Bai 2017

6/2017 Ruben Rellan-Alvarez
Lee, C-R, et al. 2017. Nature Ecology and Evolution. 1:119
   Young inversion with multiple linked QTLs under selection in a hybrid zone

Chromosomal inversions are chromosomal rearrangements that can span several Mb and have been described in several organisms from Drosophila to maize. Inversions suppress recombination and can favor local adaptation and speciation if they capture favorable alleles since. Its not clear though if favorable alleles accumulate in older inversions or, as the Kirkpatrick Barton model proposes, inversions capture chromosomal blocks that contain pre-existing adaptive alleles. In this paper, Cheng-Rui Lee, show that in a hybrid speciation zone with ecologically different subspecies (East and West) of Boechera stricta a young inversion arose after the last glaciation, quickly reached high frequency and shows signs of positive selection. The authors used a cross of collinear haplotypes to show that the inversion carries several QTLs that influence several phenological and developmental traits and controls high percentages of the phenological differences between the two subspecies. In summary this paper shows that inversions can capture pre-existing, favorable, linked QTLs during initial steps of speciation. Ruben Rellan, 2017

Complete author list: Cheng-Ruei Lee, Baosheng Wang, Julius P. Mojica, Terezie Mandáková, Kasavajhala V. S. K. Prasad, Jose Luis Goicoechea, Nadeesha Perera, Uffe Hellsten, Hope N. Hundley, Jenifer Johnson, Jane Grimwood, Kerrie Barry, Stephen Fairclough, Jerry W. Jenkins, Yeisoo Yu, Dave Kudrna, Jianwei Zhang, Jayson Talag, Wolfgang Golser, Kathryn Ghattas, M. Eric Schranz, Rod Wing, Martin A. Lysak, Jeremy Schmutz, Daniel S. Rokhsar & Thomas Mitchell-Olds.

6/2017 Fang Bai
Garcia, NS et al. 2017. Proc Natl Acad Sci, USA 114:5165-5170
   Maize defective kernel mutant generated by insertion of a Ds element in a gene encoding a highly conserved TTI2 cochaperone

The maize transposable elements Ac/Ds have been widely exploited and used in maize genetic research since it was discovered by Barbara McClintock over 50 years ago. Recently, Ac/Ds were modified by tagging the Ds elements with a green fluorescent protein (GFP) and editing the 5' and 3' sites with the Ac recognition sequence (Dsg). In this paper, Garcia et al. isolated and characterized an embryo-lethal mutant dek38-Dsg from Dsg collection. The authors took the advantages of the Dsg system to sort the wild types, heterozygotes and mutant seeds. The reciprocal cross between the mutant and WT showed the reduced male transmission. Garcia et al. found that dek38 encodes a TTI2 (Tel2-interacting protein 2) molecular cochaperone which is the homolog of yeast and Mammalian Tie2. They did the yeast two-hybrid experiment and showed that TTI2 interact with maize TTI1 and Tel2 to form the TTT complex which indicates the conserved roles of TEL2, TTI1, and TTI2 in eukaryotes. Fang Bai 2017

6/2017 Lin Li
Tai, F, et al. 2016. Plant Cell, Tissue and Organ Culture (PCTOC). 124:459-469
   ZmCIPK8, a CBL-interacting protein kinase, regulates maize response to drought stress

Plants/crops are more likely to encounter harsh environments under the global climate change. Identification of functional genes underlying stress tolerance is a key step for the improvement of stress tolerance during plant breeding. It has been reported that CBL-interacting protein kinases play an important role in plant stress tolerance. This study has cloned a novel CIPK gene. Subsequent bench works including expression analysis, Yeast two-hybrid assay, BiFC, and plant transformation, provided the evidences that it may be involved in plant response by regulating stress-related genes such as ZmCBL1, ZmCBL4 and ZmCBL9 etc. This paper has been nominated as one of the 180 groundbreaking articles that would change our world by Springer Nature Editors-in-Chief in 2016. Lin Li, 2016

cipk8 expression is greatly increased in drought conditions. Overexpression of maize cipk8 in tobacco enhances tobacco's resistance to drought stress

5/2017 Fang Bai
Rosa, M et al. 2017. Plant Cell 29:474-490
   The maize MID-COMPLEMENTING ACTIVITY homolog CELL NUMBER REGULATOR13/NARROW ODD DWARF coordinates organ growth and tissue patterning

Maize leaf is a classic system to study the organogenesis due to its distinct cell division, differentiation, and the pattern formation during the leaf development. One of the main projects in Dr. Sarah Hake lab is to study the genes and their functions underlining the leaf development. In this paper, Rosa et al. characterized a mutant called narrow odd dwarf (nod), which was discovered from EMS screening. The thorough phenotype analysis showed that nod mutants has a pleiotropic phenotypes in both vegetative and reproductive development such as dwarf bushy-like adult plants, reduced leaf dimension, and the abnormal cell division and expansion, etc.. Positional cloning found that nod encodes the maize MCA protein, a PLAC8-containing protein previously annotated as CNR13. Mosaic analysis indicates nod function cell-autonomously at the cellular and organ level. Through the RNA-seq analysis in nod mutant compared to their wild type controls, Rosa et al. demonstrated that the nod involves multiple molecular pathway such as hormone metabolism, phase-change regulation, and pathogen defense etc.. They proposed that nod regulates the cell activities by integrate both intrinsic and environmental cues. Fang Bai 2017.

5/2017 Jason Wallace
Bian, Y; Holland, JB. 2017. Heredity. 0:doi: 10.1038/hdy.2017.4
   Enhancing genomic prediction with genome-wide association studies in multiparental maize populations

Genomic prediction promises to accelerate crop improvement by letting breeders predict phenotypes from genotypes. Bian & Holland tested how including GWAS-identified markers in genomic prediction schemes would affect prediction using both simulated and real data from the maize Nested Association Mapping population. With oligogenic traits (10 simulated QTL and real disease resistances), including GWAS results significantly increased the accuracy of genomic prediction. However, with polygenic traits (100 simulated QTL and real plant height) prediction accuracy did not improve, and under some circumstances actually dropped. The authors conclude that the proper pipeline for analysis is trait-specific, and exploratory analyses to determine trait architecture would help determine the best methods to use. Their simulated data also revealed a strong coupling between between false discovery rate and power to identify true QTL, so that it was impossible to choose a truly optimal threshold for GWAS analysis. For genomic prediction, however, using the Bonferroni-corrected cutoff worked well. Jason Wallace, 2017

5/2017 Lin Li
Bouchet, S et al. 2017. Heredity 118:249-259
   Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

Maize grain yield in US has increased eight-fold in the past 80 years, of which half was contributed by breeding. Although high grain yield per plant is a primary breeding goal, the gain of maize grain yield is largely due to higher plant density. As plant density increased, maize plant morphology has been dramatically altered to optimize lights penetration into the plant canopy. Previous studies usually focused on single or a few morphology traits for the genetic dissection of maize plant morphology variation. Here, the authors assessed the genetic architecture of 24 morphology related traits in a European association mapping panel consisting of 336 diversity maize lines. Association mapping identified 34 QTLs for individual traits and six for trait cluster generated by PCA analysis. Two major observations seem very interesting: one is that only a few (5) QTL were pleiotropic although there was high correlations between these 24 morphology traits; the other is that developmental traits such as tillering, leaf number were likely to be controlled by higher number of detectable QTLs with larger individual QTL effects than growth influenced traits such as Ears per plant, Kernel row number. These results further our understanding of plant morphology diversity, which may benefit maize breeding in the future. Lin Li, 2017

4/2017 Ruben Rellan-Alvarez
Fustier, M-A, et al. 2017. Mol Ecol. 0:doi: 10.1111/mec.14082
   Signatures of local adaptation in lowland and highland teosintes from whole genome sequencing of pooled samples

Teosinte, the ancestor of maize, grows in a range of environments in M��xico. Teosinte parviglumis (Zea mays ssp parviglumis) is more prevalent in lowland regions while teosinte mexicana (Zea mays ssp mexicana) occupies highland (>2000 masl) territory. Admixture between parviglumis and mexicana can occur at mid-elevations. In this paper, the authors sampled an altitudinal gradient of teosinte populations and the used pooled sequencing populations of low, mid and high elevations. The authors used two population differentiation methods and correlations of allele frequencies with environmental variables to find outlier SNPs that tended to cluster together and 47 candidate regions were identified. The authors were able to recover a previously characterized inversion in chromosome 1. A soft sweep was found in a locus involved in leaf macrohair variation, a phenotype that is characteristic of teosinte mexicana and that is absent in lowland, teosinte parviglumis. Finally several outlier SNPs colocalized with loci involved in root system architecture, heavy metal tolerance and nutrient deficiencies point to a significant role of soil physico-chemichal properties as major drivers of teosinte local adaptation. Ruben Rellan, 2017

4/2017 Lin Li
Zhang, X, et al. 2017. Plant Physiol. 173:1554-1564
   High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth

With increasing demand to accelerate progress in crop breeding for novel traits, the plant research community needs to accurately measure increasingly large numbers of plants and plant traits. Compared with the progress of the large-scale characterization of plant genomes, there is a phenotyping bottleneck hampering progress in both knowledge and application-oriented research in crops. The authors in the paper employed a automatic phenotyping platform to profile over 100 traits across 16 developmental stages in a maize RIL population. Subsequent quantitative analyses of these traits identified ~1000 QTLs underlying agronomic traits and revealed the dynamic genetic architecture of maize plant growth. This study may provide a new strategy to breed plants that can better adapt to low input agriculture and resource-limited environments. Lin Li, 2017

This paper identifies 938 QTLs or 42 investigated phenotypic traits across 16 time points of maize growth

4/2017 Jason Wallace
Karn, A et al. 2017. G3 7:1157-1164
   Genetic analysis of teosinte alleles for kernel composition traits in maize

Starch, protein, and oil are the three major components of maize kernels and they have been under strong selection during both maize domestication and improvement. Karn et al. used a set of 10 near-isogenic line (NIL) families consisting of 3% teosinte in a B73 background to investigate the effect of ancestral teosinte alleles on kernel composition. They found 8 QTL that significantly affected kernel composition, six of which matched QTL found for the same traits in the maize Nested Association Mapping population (Cook et al 2012, Plant Phys 158:824-834) and two of which are novel. Many allelic effects were stronger in these NILs than in NAM, indicating that teosinte could serve as a source of useful alleles to introgress into modern germ plasm. Jason Wallace, 2017

4/2017 Fang Bai
Gault, CM, et al. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1616173114
   Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development

There are two types of spliceosomes involved in the RNA slicing in the eukaryotic cells, the major spliceosome of U2-type which will remove the U2-type intron and the minor spliceosome of U12-type which will remove the U12-type intron. Rgh3 is the maize ortholog of the human ZRSR2 RNA splicing factor that is identified several years ago by Dr. A. Mark Settles lab. Rgh3 affects the seed development and plant viability and the endosperm cell differentiation in rgh3 mutants is defective and delayed. In this study, Gault et al. did the RNA-seq in normal and rgh3 seedlings and roots, and tested the minor splicing in rgh3 compared to the normal siblings. The authors showed the disrupt of both the U12 splicing and the localization of the U2AF2 in mutant rgh3 allele which is similar to the human ZRSR2. The results demonstrated the conserved role of the protein RGH3/ZRSR2 across the kingdom. RT-PCR analysis using RNA extracted from total, nuclei, and polysome fractions of normal and rgh3 samples showed that some mis-spliced transcripts in rgh3 are likely to be translated. The significant finding in this study is that the authors showed extensive conservation between maize and human U12-type intron-containing genes. Fang Bai 2017

4/2017 Fang Bai
Martinez, P; Luo, A; Sylvester, AW; Rasmussen, CG. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1619252114
   Proper division plane orientation and mitotic progression together allow normal growth of maize

Symmetrically and asymmetrically cell division contributes to the cell polarity, cell shape and function, tissue formation and organ development. The TANGLED1 (TAN1) is originally identified in maize and function in the proper division plane orientation in dividing cells. In this study, Martinez et al. examined the time-lapse imaging and division-time quantification of the TAN1���YFP on the dividing tan1 cells and their normal sibling cells, and showed that TAN1���YFP was recruited to the division site after the preprophase band (PPB) formation. Their experiment of transformed tan1 with TAN1���YFP fully rescued the mutant phenotype or partial rescued with D-TAN1-13���YFP. The authors also crossed the YFP-TUBULIN into tan1 mutants to show that tan1 mutants had a phragmoplast guidance defect which resulted in the defects in division plane orientation of tan1 mutant. The significance of this research is that the authors directly demonstrated the correct division plane orientation is critical factor for the proper plant growth. Fang Bai 2017

3/2017 Philipp Weckwerth
Waters, AJ, et al. 2016. Plant J. 0:DOI: 10.1111/tpj.13414
   Natural variation for gene expression responses to abiotic stress in maize

The authors are investigating differential gene expression after abiotic stress (cold and heat) in diverse maize inbreds B73, Mo17, Oh43, PH207 and B37. They are putting an emphasis on cis- as well as trans- regulatory elements, as these require concerted action to fully mount abiotic stress responses. For their study, they used 14-day-old maize seedlings. As anticipated a large number of genes were identified that responded differentially to stress. Remarkably, there are also a large number of genes that are different between parental inbred. RNA sequencing was also performed on similar tissues of the F1 hybrids produced by crossing B73 and three other inbred lines (Mo17, PH207, Oh43). The F1 hybrids were further analyzed to evaluate allele-specific transcript abundance. This helped in assessing the abundance of cis- and trans-regulatory variation between genotypes for both steady-state and stress-responsive expression differences. Though cis-regulatory variation was more common for both steady-state and stress-responsive expression differences, some examples of trans-regulatory variation were observed. The results provided may be useful to develop predictive models for gene expression responses. The RNAseq data is available at NCBI under PRJNA244661. Philipp Weckwerth, 2017

Data Available:

3/2017 Jason Wallace
Hirsch, CN, et al. 2016. Plant Cell. 0:doi: 10.1105/tpc.16.00353
   Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Download the assembly here:

Sequence data from this article can be found in the Sequence Read Archive at the National Center for Biotechnology Information under accession number PRJNA258455. The PH207 genome multifasta file, GFF annotation file, transcript multifasta file, and protein multifasta file are available for download from the Dryad Digital Repository (DOI: 10.5061/dryad.8vj84). Additionally, the PH207 genome assembly results as Integrative Genomics Viewer (Broad Institute) tracks are available for public access at

It is well known that the maize B73 reference genome captures only part of the total diversity in the maize pan-genome. Hirsch et al. describe the sequencing and assembly of PH207, an elite inbred line from the Iodent heterotic pool. Multiple comparisons show that the PH207 assembly is of similar quality to the existing B73 genome, and comparisons between them show large amounts of structural variation between the two. Over 2500 genes were absent in one genome relative to the other ("presence-absence variants", or PAVs), and 136 gene families showed large amounts of expansion or contraction on one line relative to the other. PAVs were enriched in the pericentromeric regions, showed lower overall expression and more tissue-specific expression, and were enriched for functions related to stress responses. The two subgenomes from maize's ancient tetraploidization also showed extensive differential fractionation between the two lines. The large amount of genetic and transcriptomic differences between B73 and PH207 supports the idea that heterosis between maize lines may be driven by these line-specific variations. Comparison between these genomes highlights the importance of having multiple representative genomes for a species; additional maize genomes will doubtless be similarly useful in analyzing the variation present across maize germ plasm. Jason Wallace, 2017

3/2017 Ruben Rellan-Alvarez
Romero-Navarro, JA et al. 2017. Nature Genetics 49:476-480
   A study of allelic diversity underlying flowering-time adaptation in maize landraces

There are currently no comments for this article.

3/2017 Lin Li
Kong, FY et al. 2017. Molecular Plant 10:516-519
   Regulation of leaf angle by auricle development in maize

Plant architecture is one of most important agronomic traits associated with grain yield in maize. The leaf angle is one of the major components of plant architecture, that affects plant density in the field, while the auricle, a hinge linking the leaf blade to the vertical stem, may affect leaf angle. However, the molecular association between auricle and leaf angle has not been fully demonstrated. The authors measured leaf angle and different properties of auricle across 102 diverse maize inbreds, and conducted RNA-Seq on auricles at early, middle, and late developmental stages in both B73 and 986 at V3 stage. The morphogenesis analysis indicates that the leaf auricle has a crucial effect on LA in a large population of maize inbred lines, and the diversity of auricle development contributes to LA in maize. Meanwhile, the transcriptomic analyses show that genes associated with cell division and elongation might be involved in auricle development, which provides novel insight of the molecular mechanisms determining LA and plant architecture in maize. Lin Li, 2017

This letter to the Editor contains information on RNA-seq and more genes, but lacks primary data and reference to data repository.

3/2017 Fang Bai
Kelliher, T, et al. 2017. Nature. 542:105-109
   MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction

Doubled haploid breeding is one of the most efficient ways to shorten breeding time and improve the crop uniformity. To study the developmental genetics underlying the haploid induction in maize, Kelliher et al. (2017) generated BC1 mapping populations by cross the Stock 6 derivative RWK to the inbred NP2460 and NP2391, and then backcrossed to the RWK. Combined with the fine mapping and sequencing data of the candidate genes, they found that a loss-of-function mutation in GRMZM2G471240 is responsible for the haploid induction. MATRILINEAL (MTL) encodes a patatin-like phospholipase and specifically locates in the cytoplasm of the male gametes. The novel edits in MTL lead to a 6.7% haploid induction rate. This discovery may lead to the in vivo haploid induction in economic crop breeding in the near future. Fang Bai, 2017

2/2017 Jason Wallace
Jamann, TM; Sood, S; Wisser, RJ; Holland, JB. 2017. PLoS One. 12:e0168910
   High-throughput resequencing of maize landraces at genomic regions associated with flowering time

Whole-genome sequencing provides a wealth of data but can be overkill for researchers interested in only specific genetic regions. Jamann et al. describe the development of a multiplex PCR Ampliseq procedure to amplify and sequence a total of 72 kb across 20 genes related to maize flowering time (including vgt1, ZmCCT, and other high-confidence candidate genes). The authors used a total of 319 primer pairs multiplexed in two PCR reactions to amplify these regions across three maize inbreds, two hybrids, and 19 landraces; amplicons were then sequenced using IonTorrent technology. After tuning their SNP-calling pipeline, they had high sensitivity for calling reliable genotypes, including heterozygotes, and used them to identify genetic relationships among the maize samples. The authors estimate that one could use this method to interrogate 2-5 times as much genomic space and still maintain quality genotypes. Jason Wallace, 2017

Whole-genome sequencing provides a wealth of data but can be overkill for researchers interested in only specific genetic regions. Jamann et al. describe the development of a multiplex PCR Ampliseq procedure to amplify and sequence a total of 72 kb across 20 genes related to maize flowering time (including vgt1, ZmCCT, and other high-confidence candidate genes). The authors used a total of 319 primer pairs multiplexed in two PCR reactions to amplify these regions across three maize inbreds, two hybrids, and 19 landraces; amplicons were then sequenced using IonTorrent technology. After tuning their SNP-calling pipeline, they had high sensitivity for calling reliable genotypes, including heterozygotes, and used them to identify genetic relationships among the maize samples. The authors estimate that one could use this method to interrogate 2-5 times as much genomic space and still maintain quality genotypes. Jason Wallace, 2017

Gene Models from this paper: GRMZM2G154580, GRMZM2G011357, GRMZM2G180190, GRMZM2G095598, GRMZM2G033962, GRMZM2G031432, GRMZM2G031432, GRMZM2G031432, GRMZM2G031432, GRMZM2G045275, GRMZM2G067921, GRMZM2G179264, GRMZM2G700665, GRMZM2G405368, GRMZM2G085218, GRMZM2G038783, GRMZM2G359322, GRMZM2G092174, GRMZM2G381691

NCBI Sequence Read Archive SRA504653 (raw sequence read data):

2/2017 Fang Bai
Xu, GH, et al. 2017. New Phytol. 0:doi: 10.1111/nph.14400
   Complex genetic architecture underlies maize tassel domestication

Maize has two types of inflorescences: the male inflorescence of tassel and the female inflorescence of ear. The architecture of the tassel is important for improving the crop yield and studying the maize domestication. In this paper, Xu et al. (2017) perform high resolution of quantitative trait loci (QTL) mapping on five tassel traits in the maize-teosinte BC2S3 population and identified 11 loci for tassel length,17 for tassel branch length, 12 for tassel peduncle length, 14 for tassel branch number, and 18 for tassel branch angle. They also found many known inflorescence architecture genes are in their QTL mapping region which indicate gene roles in tassel evolution and maize domestication. In addition, Xu et al. found that several known flowering time genes are also in the tassel QTL region and those flowering time genes might be involved in the natural variation during the tassel evolution. Fang Bai, 2017

2/2017 Philipp Weckwerth
Wang, Y et al. 2016. Frontiers Plant Sci 7:1654
   The Mechanisms of Maize Resistance to Fusarium verticillioides by Comprehensive Analysis of RNA-seq Data

The authors are reporting on RNA-seq data acquired from Kernels treated with Fusarium verticillioides of a highly resistant maize variety (BT-1). F. verticillioides is one of the most commonly reported fungal species responsible for ear rot in maize, which also leads to substantial accumulations of mycotoxins. By performing RNA-seq on F. verticillioides treated kernels the authors show that the resistance of BT-1 is due to induced transcription of genes associated with pathogen recognition and sub sequential responses, e.g. enhanced formation of secondary cell wall. Differential gene expression in susceptible (N6) and resistant (BT-1) maize varieties was confirmed by qRT-PCR and microarray. Interestingly, some of the genes strongly induced by F. verticillioides in the resistant variety BT-1 are associated with QTLs of ear rot resistance identified in previous studies, opening up the field to promote the identification of genes involved in ear rot resistance. The authors state in the paper that the RNA -seq data is submitted to NCBI, and is now accessible here: Philipp R Weckwerth, 2017

1/2017 Jason Wallace
Yendrek, CR, et al. 2017. Plant Physiol. 173:614-626
   High-throughput phenotyping of maize leaf physiology and biochemistry using hyperspectral reflectance

There is a big push to develop rapid, high-throughput methods to phenotype traits in the field. Although there is much hype and expectation about different methods, in many cases it's unknown how well they will work in practice. Yendrek et al. Provide an analysis of hyperspectral reflectance data taken across a maize field under both normal and high-ozone (stressful) conditions. The data were collected by hand, which while not as high-throughput as a tractor- or drone-mounted system was still many times faster than the wet-lab sampling used to get the ground-truth data. Partial least-squares regression on the spectra were able to predict 5 out of 7 tested traits with good accuracy: chlorophyll content, nitrogen content, specific leaf area, photosynthesis rate, and sucrose. The two poorly predicted phenotypes were PEP carboxylation and oxygen radical absorbance capacity. Statistical analyses of the model-predicted phenotypes showed similar results to the true values, indicating that using hyperspectral imaging to monitor plants for these traits is could replace traditional wet-lab analysis, at least for routine use. Jason Wallace, 2017

1/2017 Philipp Weckwerth
Oliveira-Garcia, E; Deising, HB. 2016. Plant J 87:355-75
   Attenuation of PAMP-triggered immunity in maize requires down-regulation of the key β-1,6-glucan synthesis genes KRE5 and KRE6 in biotrophic hyphae of Colletotrichum graminicola

The authors functionally characterize KRE5 and KRE6, key enzymes in β-1,6-glucan synthesis, of the ascomycete Colletotrichum graminicola, a hemibiotroph that infects maize (Zea mays). After appressorial plant invasion, this fungus sequentially differentiates biotrophic and highly destructive necrotrophic hyphae. RNAi-mediated reduction of KRE5 and KRE6 transcript abundance causes appressoria to burst and swelling of necrotrophic hyphae, indicating that β-1,6-glucosidic bonds are essential in appressoria and necrotrophic hyphae. As RT-qPCR is not feasible due to unsynchronized differentiation of infection structures of C. graminicola, the authors used live cell imaging employing KRE5:mCherry and KRE6:mCherry knock-in strains and probing of infection structures with a YFP-conjugated β-1,6-glucan-binding protein. This revealed expression of these genes and exposure of β-1,6-glucan in conidia, appressoria and necrotrophic, but not in biotrophic hyphae. In contrast, overexpression of KRE5 and KRE6 in biotrophic hyphae leads to activation of broad-spectrum plant defense responses, including papilla and H2O2 formation, as well as transcriptional activation of several defense-related genes. The results suggest that down-regulation of synthesis and avoidance of exposure of branched β-1,3-b-1,6-glucan in biotrophic hyphae is required for attenuation of plant immune responses. Philipp Weckwerth, 2017

1/2017 Lin Li
Huang, XH. 2016. Nature. 537:629-633
   Genomic architecture of heterosis for yield traits in rice

Heterosis or hybrid vigor, usually refers to the phenomenon that hybrid offspring exhibit superior performance relative to that of their parents. Heterosis has been of immense economic value in agriculture, especially for the utilization in maize and rice. Despite extensive investigation, the molecular mechanism underlying heterosis remains elusive. It appears that there is not a single gene or mechanism but many genes or mechanisms associated with heterosis. In this study, the authors describes a comprehensive experiment, collecting ultra-high density of marker data and precise phenotypic data in 10,074 F2 lines from 17 representative hybrid rice crosses. Although this is still a QTL study, this study suggests that most heterozygous loci exhibit positive partial dominant effect, while a few loci with pseudo-overdominant or overdominant effect, contributing to the heterosis in hybrids. Most interestingly, a small number of genomic loci from female parents could explain a large proportion of heterosis. Such dominant parental effect has also been observed in the study in maize from Schnable group (Swanson-Wagner et al., 2009). This paper provides a clue to conduct heterosis dissection with the rapid progress of next generation sequencing and phenotyping in maize. Lin LI, 2017

1/2017 Fang Bai
Gontarek, BC; Neelakandan, AK; Wu, H; Becraft, P. 2016. Plant Cell. 0:doi: 10.1105/tpc.16.00609
   NKD transcription factors are central regulators of maize endosperm development

During the seed growth, the endosperm supplies nutrients and signals to promote embryo development and seed germination. NAKED ENDOSPERM1 (NKD1) and NKD2 are duplicate genes which are INDETERMINATE DOMAIN (IDD) transcription factors important for maize endosperm development. In this paper, Gontarek et al. (2016) study the function of NKD1 and NKD2. Through the RNAseq experiment from endosperm of nkd1nkd2 mutant compared to the wild type, they found that NKD 1 and NKD2 regulate genes involved in a broad biological processes, such as hormone regulation, cell division and differentiation, starch accumulation and seed maturation, etc.. The authors performed Selection and amplification binding (SAAB) and Electrophoretic mobility shift assays (EMSAs) to identify 8-bp binding sequence (BCS) of [TA]-T-[TCG]-G-T-[CGA]-G-T for NKD1 and 6bp BCS of T-G-T-[CT]-G-[TG] for NKD2. Furthermore, they analyze the direct target genes of NKD1 and NKD2. Through a series of experiment, they showed that NKD1 and NKD2 work as homodimer and heterodimer mediated by the ID domain. Fang Bai, 2017.

1/2017 Ruben Rellan-Alvarez
Renny-Byfield, S et al. 2017. pp.10.1093/molbev/msx121 in Mol Biol Evol
   Gene fractionation and function in the ancient subgenomes of maize

After maize genome duplication many paralogous genes have been lost and many returned to single copy status of the subgenomes (maize1) has been less affected by fractionation than the other (maize2). It has been hypothesized that higher expressed paralogs should have a higher effect on the phenotype and therefore belong to the less fractioned subgenome. In this manuscript Renny-Byfield, Rodgers-Melnick & Ross-Ibarra use publicly available gene expression, phenotypic and epigenetic data test this hypothesis that higher expression genes. They found that maize1 paralogous genes explain more phenotypic variability ((measured as higher heritability) than their maize2 counterparts, that in general this corresponds with higher expression levels of maize1 paralogs and that this could be explained at least in part by higher levels of methylation in the maize2 subgenome genes. One unexpected result from their analysis is that maize1 singleton genes (lacking a paralogous copy) explain more phenotypic variability than maize2 genes even thought they have comparable expression levels. Ruben Rellan, 2017

12/2016 Yan He
Dong, XM, et al. 2016. Molecular Plant. 0:doi: 10.1016/j.molp.2016.10.007
   Dynamic and antagonistic allele-specific epigenetic modifications controlling the expression of imprinted genes in maize endosperm

Genomic imprinting, a classic epigenetic phenomenon, arises from allele-specific epigenetic modifications that are established during gametogenesis. The current knowledge have suggested that DNA methylation and H3K27me3 have plays critical roles in regulating genomic imprinting, however, little is known about how the contributions of allele-specific active histone modifications to imprinting in plant. In this study, the authors have identified 337 allele-specific H3K4me3 and H3K36me3 peaks in endosperm. The results showed that paternally expressed genes (PEGs) are mostly co-localized with paternally preferred H3K4me3 and H3K36me3, and vice versa, maternally expressed genes (MEGs) were usually associated with maternally preferred H3K4me3 an H3K36me3 peaks. Interestingly, the active H3K4me3, H3K36me3 and repressive H3K27 were present together in parts of PEGs. For constitutive PEG, H3K27 and H3K36me3 were specifically deposited on hypomethylated maternal alleles and hypermethylated paternal alleles. DNA methylation and H3K4me3 were specifically marked on paternal and maternal alleles around TSS of endosperm MEGs (endo-METs), respectively. In addition, a set of maternally expressed non-coding RNAs (MNCs) showed same allele-specific epigenetic features with endo-MEGs, indicated that a similar mechanism in regulating imprinted genes and non-coding RNAs. These results enhance the understating of the complex patterns depicting mutually exclusive epigenetic modifications associated with different alleles of imprinted genes which may have active roles for the development of maize endosperm. Yan He, 2016

12/2016 Eli Rodgers-Melnick
Svitashev, SK et al. 2016. Nature Communications 7: 13274
   Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes

The recent successes of CRISPR/Cas9 genome editing in plants have generated a wave of excitement within commercial agriculture. However, the implementation of Cas9-delivered genome edits within product-driven breeding programs faces several challenges. In particular, off-target mutations must be minimized, both to avoid deleterious side-effects for the plant and to facilitate regulatory approval for the edited product. In a number of species, including several plants, delivery of a pre-loaded Cas9-gRNA ribonucleoprotein complex to the cell was shown to minimize off-target effects. However, previous RNP transformations in plants were limited to protoplasts, which rarely regenerate fertile plants among most crop species, including maize. In this study, authors Svitashev et al demonstrate the delivery of Cas9-gRNA RNPs to maize immature embryo cells through bombardment with a helium gene gun. The authors show that although the frequency and composition of the target-site mutations is similar between the RNP-based and DNA vector-based methods, off-target mutations at a known site for the DNA vector approach were nearly or completely eliminated under the RNP approach. Furthermore, the high efficiency of RNP-directed edits permits recovery of the 2-10% of plants containing edits in the absence of selectable markers. Thus, genomic editing of crop species may be achieved without the need for a selective media or the additional step of back crossing to eliminate off-target mutations. Eli Rodgers-Melnick, 2016

12/2016 Carolyn Rasmussen
Nannas, NJ; Higgins, DM; Dawe, RK. 2016. J Cell Sci. 129:4014-4024
   Anaphase asymmetry and dynamic repositioning of the division plane during maize meiosis

In this study, the authors describe a phenomenon observed during meiosis: metaphase and anaphase spindle asymmetry in the cell that is corrected by higher chromosome movement rates and longer distances. CFP-TUBULIN was used to label the microtubule structures while SYTO12, a live cell dye that binds nucleic acids, was used to label the chromosomes. The authors looked at chromosome movements during meiosis I, when homologous chromosome were separated, and meiosis II, when sister chromatids were separated and observed that chromosomes were pulled farther apart in meiosis II than meiosis I. When the spindle was asymmetrically localized in the cell, chromosomes moved further and faster to correct their location towards the center of the cell. The phragmoplast, the plant specific cytokinetic apparatus, was then formed in between the chromosomes rather than the original spindle position, suggesting that a specific interaction occurs between chromosomes (or the cell periphery) and the phragmoplast to establish its proper location. Although there is no mechanism yet known, this paper provides insight into the factors that help position chromosomes and microtubule structures in meiotic cells. Carolyn Rasmussen, 2016

12/2016 Michelle Facette
Mir, R et al. 2016. Plant Physiol pp.doi: 10.1104/pp.16.01454
   DII-based auxin reporter in maize reveals low auxin signaling during telophase and early G1

There are currently no comments for this article.

12/2016 Arnaud Ronceret
Higgins, DM et al. 2016. Frontiers Plant Sci 7:1277
   The maize Divergent spindle-1 (dv1) gene encodes a kinesin-14A motor protein required for meiotic spindle pole organization

There are currently no comments for this article.

11/2016 Eli Rodgers-Melnick
Kadam, DC et al. 2016. G3 6:3443-3453
   Genomic prediction of single crosses in the early stages of a maize hybrid breeding pipeline

Modern maize breeding programs depend upon the optimization of single crosses between inbreds from different heterotic groups. Specific inbreds must move through several years of topcrosses to establish their general combining ability (GCA), while the latter stages of hybrid breeding program focus on discovering specific combinations of inbreds with high specific combining ability (SCA). Practically, only a small number of all possible hybrids can be tested across a program's target population of environments, so accurate prediction of single cross phenotypes is highly desirable. In this study, authors Kadam et al tested the use of single cross prediction for random sets of crosses between members of biparental families. Specifically, they made 6 biparental families from all combinations of 3 inbred lines in the Stiff Stalk Synthetic (SSS) and Non-stiff stalk (NSS) heterotic groups. They used two primary methods to estimate single-cross performance, comparing the older approach of using single cross covariance to that of using heterotic-group specific covariances to estimate GCA for all inbreds and SCA for all possible combinations. Generally, the authors find that the latter approach can lead to higher accuracy, particularly when neither inbred parent is present within the training set. Eli Rodgers-Melnick, 2016

11/2016 Michelle Facette
Wang, G et al. 2012. Plant Cell DOI 10.1105/tpc.112.10136
   Opaque1 encodes a myosin XI motor protein that is required for endoplasmic reticulum motility and protein body formation in maize endosperm

There are currently no comments for this article.

11/2016 Carolyn Rasmussen
Li, L et al. 2016. Sci. Rep. 6:34395
   Characterization of maize roothairless6 which encodes a D-type cellulose synthase and controls the switch from bulge formation to tip growth

In this paper, the authors identify roothairless6 (GRMZM2G432699) as a gene encoding a D-type cellulose synthase required for all root hair development in maize. The mutant was identified by a combination of bulked segregant RNA sequencing (BSR-Seq) and Seq-Walking. Seq-Walking uses Mutator (Mu) insertion sequences to identify the mutant locus. When the mutant is caused Mu insertion in the locus, the locus can be identified by amplifying all DNA segments flanking Mu transposon insertions from both the mutant and wild-type. These are then compared, and "mutant-specific" Mu insertions are identified. Those that were located in the mapping interval identified by BSR-Seq showed an insertion in GRMZM2G432699. Other mutant alleles confirmed the identity of the rth6 gene. rth6 mutants were able to initiate root hairs, but elongation was stalled. Not surprisingly, rth6 transcripts were most abundant in root hairs and roots when compared with other CSLD transcripts that do not play a role in root hair elongation. Finally, a model is proposed to discuss the potential role of RTH proteins in root hair elongation. RTH6, a cellulose synthase, likely extrudes cellulose at the tip to strengthen the shaft while RTH3, a COBRA-like protein organizes the cellulose and RTH2 generates hydroxyl radicals to loosen the cell-wall. Carolyn Rasmussen, 2016

11/2016 Yan He
Richter, A, et al. 2016. Plant Cell. 0:doi: 10.1105/tpc.15.00919
   Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays

Plant volatiles play important roles in defense against herbivores, fungi and bacteria, as well as in signaling interaction between plant and other organisms. However, it is not fully known about how the biosynthetic and the regulation pathway of every individual plant volatile in response to external stimuli. In this work, the authors utilized genome-wide association study (GWAS) in a nested association mapping panel (NAM) to exploit the natural variation of herbivore-induced volatiles. The results yield a set of quantitative trait loci (QTLs) controlling the variation in the production of volatile terpene. The most significant SNPs associating the emission of (E)-nerolidol, linalool, DMNT and TMTT fall into the promoter of the gene encoding the terpene synthase TPS2 (GRMZM2G046615). The biochemical experiments later demonstrate that TPS is responsible for the production of volatile mono-, sesqui-, and diterpene alcohols. Furthermore, the joint-linkage analysis identified two cytochrome P450 genes (GRMZM2G102079 and GRMZM2G139467) are capable of converting nerolidol into DMNT by oxidative degradation. In conclusion, the identified two monooxygenases and the associated DMNT biosynthetic pathway are distinct from those previously characterized DMNT and TMTTT synthsis in Arabidopsis, implying that the independent evolution of these enzymatic activities. Yan He, 2016

11/2016 Arnaud Ronceret
Yang, CJ et al. 2016. Genetics 204:1573-1585
   A gene for genetic background in Zea mays: fine-mapping enhancer of teosinte branched1.2 to a YABBY class transcription factor

There are currently no comments for this article.

10/2016 Yan He
Yao, DS, et al. 2016. PLoS Genetics. 12:e1006270
   Maize opaque10 encodes a cereal-specific protein that is essential for the proper distribution of zeins in endosperm protein bodies

Cereal storage protein are valuable nitrogen sources for human and livestock. Prolamins are the major storage proteins and deposited into protein bodies (PBs) that occur only in cereal gain endosperm. In this study, the authors used the strategy of the positional cloning to identify the gene underlying the Maize opaque10 (o10), a classic opaque endosperm mutant. The results showed that o10 encodes a novel cereal-specific PC protein. A detailed characterization of its functional domains revealed that its middle domain is responsible for its dimerization and its C-terminus is required for its ER localization and PB deposition, and its N-terminus is facilitating the formation of a ring-shaped layer in PBs through direct interaction with two major storage proteins (22-kD and 16-kD zeins). The loss-of-function of o10 caused the disruption in this ring-shaped distribution of 22-KD and 16-kDzeins, leading to the presence of misshapen PBs. These results demonstrated O10 protein is essential for PB morphology by regulating the ring-shaped distribution of 22-kD and 16-kD in maize endosperm. Yan He, 2016

10/2016 Arnaud Ronceret
Koo, DH; Zhao, H; Jiang, JM. 2016. Chromosome Res. 0:10.1007/s10577-016-9537-5
   Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH

Tandemly repetitive DNA (satellite) are major component of heterochromatin. In maize, they are organized in long array in knobs, centromeric, pericentromeric and telomeric regions. This paper describes the detection of chromatin associated transcripts of four common of these satellite repeats by RNA-FISH. Bioinformatics analysis of the maize ESTs and mRNA seq database detect the presence of -low abundant or poorly recovered- transcripts associated with these satellites. RNAse treatment, competition with unlabeled probe and comparison with FISH signal confirmed the identification of the RNA signal in the nuclei. The 180bp knob repeats show transcripts associated with minor 180bp foci on interphase nuclei suggesting that they are transcribed from the small knobs loci. The RNA-FISH technique did not detect any transcript of the 350bp subtelomeric repeat. The telomeric (TTTAGGG)n show both sense and antisense RNA signal with more foci (10 to 15 per nucleoplasm) with probe detecting the (UUUAGGG)n containing RNA molecules than for (CCCUAAA)n (3 to 6 per nucleoplasm). This telomeric strand specific RNA-FISH pattern was also found in tobacco nuclei. The centromeric 156bp CentC repeat shows sense and antisense transcripts. RNAse treatment comparison analysis show that these structural heterochromatic RNA participate in the proper localization of nucleolar fibrillarin and the kinetochore protein MIS12 but does not affect the localization of CENH3. The paper suggests that an essential and functional component of heterochromatin could be based on structural RNA expressed from satellite. Arnaud Ronceret, 2016

10/2016 Eli Rodgers-Melnick
Ko, DK, et al. 2016. PLoS Genetics. 12:e1006197
   Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids

In maize, approximately 10% of genes display oscillating expression patterns consistent with regulation by a circadian clock. Thus, any alterations to master regulators of circadian rhythms have the potential to promote major, systematic effects. Authors Dae Kwan Ko et al investigate the roles of the 2 maize homologs of CIRCADIAN CLOCK ASSOCIATED1 (CCA1), a master circadian regulator with associations to enhanced photosynthetic activity and biomass accumulation in Arabidopsis thaliana. The authors demonstrate a phase-shift in the binding of ZmCCA1 toward the morning hours in B73-Mo17 hybrids relative to inbreds, which is also associated with non-additive gene expression of the putative regulated genes during seedling developmental states. The amplified early induction of many genes - particularly those involved in carbon fixation - may have a direct role in producing the strong hybrid vigor forming the basis of modern commercial maize production. Eli Rodgers-Melnick, 2016

10/2016 Carolyn Rasmussen
Lowe, KS et al. 2016. Plant Cell pp.10.1105/tpc.16.00124
   Morphogenic regulators baby boom and wuschel Improve monocot transformation

Overexpression of two embryogenic tissue promoting genes, Babyboom (Bbm) and Wuschel2 (Wus2), vastly increased transformation efficiency of maize lines that were previously difficult or impossible to transform. In addition, use of Bbm and Wus2 together allowed efficient transformation and eventual recovery of transformed plants from typically difficult starting materials including the embryos in mature seeds and seedling leaf tissue as well as transformation of sorghum, rice and sugar cane material. The Bbm and Wus2 cassette prevented successful regeneration so the authors cleverly designed removal of the Bbm and Wus2 cassette using Cre-lox mediated recombination controlled by a drought inducible promoter. The major drawback is that many of the plasmids used in this article contain selectable markers that may require multiple material transfer agreements. However, the probable utility of this cassette for transformation of more maize inbred lines and more flexible starting material will provide a major step forward for researchers working on maize or other monocots. Carolyn Rasmussen, 2016

Sequence data from this article can be found in the GenBank/EMBL databases under the following accession numbers: Zm-Bbm cDNA (CS155772); Zm-BBM protein (CAJ29869); Zm-Wus2 cDNA (EA275154); and Zm-WUS2 protein (ABW43772). The Os-Bbm gene can be found at OSA1 Release 7 (LOC_Os1g67410.1).

9/2016 Arnaud Ronceret
McCaw, ME et al. 2016. Genetics 204:35-42
   Fast-flowering mini-maize: seed to seed in 60 days

This article presents two new inbred lines called Fast Flowering Mini-Maize (FFMM-A and FFMM-B) developed to have better characteristics for growing maize as an experimental model in greenhouse ie: reduced plants space requirements as well as a very short life cycle for maize. The FFMM lines are of particular interest for classroom and are a new toolkit for maize genomic research. The FFMMs flower in a month and produce viable kernels two months after plantation. These allow to have 5 to 6 generations of maize a year, characteristics that can compete with the other popular plant model Arabidopsis thaliana. These inbred were generated from four early flowering founders : Neuffer's Early ACR (University of Missouri; stock #60:8), Alexander's Early Early Synthetic (; stock #94-2-7 self), Tom Thumb Popcorn (Ames, IA; accession #PI 217412), and Gaspe Flint (Ames, IA; accession #PI 214279). Selection for earliest flowering, good seed production and general plant morphology during the 11 generations of inbreeding successfully improved the FFMM characteristics for a 'research model' compare to the founders. Karyotypes and genotyping by sequencing analysis determined the genomic ancestry and relative contribution of each founder for FFMM-A and FFMM-B. The two FFMM share 41% of their genome including a shared vegetative to generative transition1 (vgt1) variant (, coming from Gaspe Flint, associated with early flowering. As expected, the remaining genome structural differences due to different founder genomic contribution allowed heterotic effects when both lines are crossed. Interestingly, in contrast to a long believed correlation between genome size and life cycle length, the authors show that the genome size of FFMM-A is larger than B73 reference genome and that of FFMM-B. This result discredits the idea that a big genome size is a limitation for a short life cycle. FFMM-A genomic information is included as sample 'MM-1A' in Maize Hapmap3. Seed stocks of the two FFMM are available through the maize genetic stock center (FFMM-A stock TX40J;; FFMM-B stock TX40K; Arnaud Ronceret, 2016

9/2016 Andrea L. Eveland
Walley, JW, et al. 2016. Science. 353:814-818
   Integration of omic networks in a developmental atlas of maize

Walley et al have published a huge proteomic atlas of maize. This will be integrated with MaizeGDB and should be a wonderful resource for all of us. Andrea Eveland, 2016

9/2016 Michelle Facette
Beydler, B et al. 2016. Plant Physiol 171:2648-2658
   The juvenile phase of maize sees upregulation of stress-response genes and is extended by exogenous jasmonic acid

There are currently no comments for this article.

9/2016 Carolyn Rasmussen
Giannoutsou, E; Apostolakos, P; Galatis, B. 2016. Planta. 0:10.1007/s00425-016-2574-7
   Spatio-temporal diversification of the cell wall matrix materials in the developing stomatal complexes of Zea mays

In this paper, the authors use antibodies against cell wall components to analyze changes in cell wall composition during stomatal development in maize. First, they define the developmental stages of stomatal development and then use specific antibodies against homogalacturonans with various levels of esterification, mixed-linkage glucans, rhamnogalacturonans and arabinogalactan proteins to determine when and where these cell wall components localize. Intriguingly, an antibody that recognizes calcium linked de-esterified or non-esterified homoglacturonans may potentially mark the location of the preprophase band, a microtubule and microfilament structure that determines the future division site in land plants. In addition, this antibody also highlights newly formed cell walls transiently during stomatal development. Arabinogalactans appear in young guard mother cells demonstrated using antibodies as well as a Yariv reagent dye. Rhamnogalacturonans recognized by the LM6 antibody decorated the walls of young guard mother cells and was observed at cell wall junctions. Overall, it is clear that molecular cues must work together with cell wall modifications to promote changes in cell shape and fate. While the specific roles of these cell wall modifications remain mysterious, this paper is an important step forward in understanding how development and cell wall modifications are integrated in maize. Carolyn G. Rasmussen, 2016

8/2016 Yan He
Wu, L, et al. 2016. Sci. Rep.. 6:30641
   Comparative proteomic analysis of the shoot apical meristem in maize between a ZmCCT-associated near-isogenic line and its recurrent parent

ZmCCT, one of the critical genes regulating photoperiod response and its active expression under long-day conditions can postpone flowering in maize. However, till now, we know very little about the functional mechanisms of ZmCCT activity. In this research, the authors investigated the deferentially expressed protein in shoot apical meristem (SAM) between a near-isogenic line (NIL) and its recurrent parent using a proteomics approach, called the isobartic tags for relative and absolute quantification (iTRAQ). In sum, 386 protein were identified and fall into multiple functional categories, including energy production, photosynthesis, signal transduction, cell organization and cell biogenesis. These proteins serve as the candidate targets regulated by ZmCCT, and the involving pathways enhance our understanding about the mechanisms of ZmCCT in regulating the photoperiod in maize. Yan He, 2016

8/2016 Carolyn Rasmussen
Sebastian, J et al. 2016. Proc Natl Acad Sci, USA 113:8861-8866
   Grasses suppress shoot-borne roots to conserve water during drought

The authors showed that several Setaria species, several maize inbred lines and other members of the Poaceae family inhibit crown root formation under water deficit conditions. Under well-watered conditions S. viridis crown roots contribute significantly to root architecture. Addition of water locally near crown roots induced rapid new crown root growth indicating that crown roots are highly responsive to water. This response is matched by a significant transcript expression differences in the crown root region in well-watered and water deficit conditions including transcripts associated with oxidative stress and sexual reproduction. Use of a maize mutant in a lateral organ boundaries domain protein which does not produce crown roots, rootless concerning crown and seminal roots, had higher shoot and soil moisture under water deficit conditions likely due to a smaller root system. The authors showed that crown root growth inhibition shows significant variability in the maize nested association mapping lines to suggesting that this may be a trait that might be modified to improve crop yield under different local water conditions. The authors uploaded their expression data into the GEO database under accession GSE78054. RTCS = GRMZM2G092542. Carolyn G. Rasmussen, 2016

8/2016 Michelle Facette
Berny, MC et al. 2016. Molecular Plant 9:986-1003
   Single mutations in the transmembrane domains of maize plasma membrane aquaporins affect the activity of the monomers within a heterotetramer

Plasma membrane intrinsic proteins (PIPs) are protein channels found in biological membranes that facilitate the transport of water and small proteins. In this paper, Berny et al. describe the stoichiometry of a heterotetramer water channel (aquaporin) and the amino acid residues required for their physical association. PIPs are subdivided into two phylogenetic groups: PIP1s and PIP2s. PIP2s are plasma membrane water channels that, through physical interactions, recruit PIP1s from the ER to the plasma membrane. Berny et al. use tagged versions of PIP1;2 and PIP2;5 to confirm that these proteins assemble as different combinations of homo- and hetero-dimers (which then associate to form homo- or hetero-tetramers). They use predictive modeling to identify residues within the transmembrane domains of PIP1;2 and PIP2;5 that may facilitate their physical interactions. Using functional assays in Xenopus oocytes, they found characterized mutations in PIP1;2 at these key residues. Since PIP1;2 does not act as a water channel when expressed alone, but does when co-expressed with PIP2;5, mutation variants were expressed both on their own and with PIP2;5 to determine their activity within home and hetero-tetramers. Additionally, they also assayed the localization of these channels in oocytes and/or maize epidermal cells. Several mutations in PIP1;2 inactivated the PIP2;5 water channel when co-expressed. Reciprocally, other mutations activated the PIP1;2 channel, promoting channel activity when PIP1;2 was expressed alone. Notably, one particular mutation activated the PIP1;2 channel when expressed alone, promoting plasma membrane (instead of ER) localization, but when co-expressed with it inhibited it's PIP2;5 activity, rather than synergistically increasing it as seen with wildtype versions. The mutational analyses here provide structural insights on the interactions between the multiple PIP isoforms, and how their assembly and localization confers water-channel activity in maize. Michelle Facette, 2016

8/2016 Eli Rodgers-Melnick
Beissinger, TM et al. 2016. Nature Plants 2:16084
   Recent demography drives changes in linked selection across the maize genome

The extant genetic diversity of a given species arises from the variation produced by mutation and recombination filtered through the interacting forces of selection and genetic drift. The dynamics of the interplay between drift and selection depend on the product of the effective population size (Ne) and the coefficient of selection (s). Thus, changes in the former over time can lead to altered patterns of genetic diversity across a species. In this study of maize and teosinte genetic diversity, authors Tim Beissinger et al use the maize HapMap2 and HapMap3 data to unravel the dynamics of how selection has differentially impacted variation in the subspecies. The authors begin by confirming that site frequency spectra significantly differ inside and outside of genes in both maize and teosinte, likely reflecting the differing impacts of selection. They then use a demographic model to estimate a split between maize and teosinte 15,000 generations ago, with an initial maize Ne 5% of the ancestral effective population size. This initial model of incorporates post-domestication exponential growth and ongoing bidirectional gene flow, resulting in a modern Ne of 370,000. However, alternative models indicate this number may be several orders of magnitude larger. Strikingly, the authors find no evidence for the widespread impact of hard sweeps, with no significant differences in the diversity surrounding missense vs. synonymous substitutions. However, the authors do find that two estimators of Ne*s, the average number of pairwise differences and the number of singletons, significantly differ in opposite directions surrounding genic regions. Specifically, pairwise diversity has a greater reduction surrounding genes in teosinte, while singleton diversity is more strongly reduced in maize. Given that extant singleton polymorphisms are more likely to have arisen during recent population expansions, these results suggest that historical purifying selection was stronger in teosinte, while the increased effective population size of modern maize leads to enhanced purifying selection against rare deleterious alleles. Eli Rodgers-Meinick, 2016

8/2016 Arnaud Ronceret
Dong, J et al. 2016. Proc Natl Acad Sci, USA 113:7949-7956
   Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

There are currently no comments for this article.

7/2016 Carolyn Rasmussen
Best, NB et al. 2016. Plant Physiol pp.DOI: 10.1104/pp.16.00399
   nana plant2 encodes a maize ortholog of the Arabidopsis brassinosteroid biosynthesis protein Dwarf1, identifying developmental interactions between brassinosteroids and gibberellins

The authors showed that nana plant2 (na2, GRMZM2G057000) encodes an enzyme required for ∆24-sterol reductase activity used in brassinosteroid biosynthesis. NA2 converts 24-methylenecholesterol to campesterol. The na2 mutants had upright leaves, short stature due to internode elongation failure as well as well as defects in flower development due to inappropriate pistil development in the tassel (tasselseed). na2 expression was ubiquitous, but particularly high in mRNA from the collar region (containing the ligule, auricle and intercalary meristem). A paralog na2-like gene (GRMZM2G455658) was poorly expressed and had frameshift mutations consistent the possibility that it encodes a pseudogene. Next the contributions of brassinosteroid (BA) and gibberellin (GA) were assessed via phenotypic characterization of combinations of mutants in BR and GA biosynthesis throughout maize development. Double mutants revealed that BR and GA function additively in plant growth, but have distinct functions in leaf angle, flower development and tillering. GA biosynthesis mutants form anthers in the ear, while BR biosynthesis mutants do not: double mutants still produce anthers in the ear indicating that this phenotype does not depend on BR synthesis. In contrast, tillering occurs in GA biosynthesis mutants, but it requires active BR biosynthesis. BR biosynthesis mutants produce tasselseeds, but double mutants do not, indicating that the tasselseed phenotype requires active GA synthesis. In addition to assessing double mutant phenotypes, exogenous GA was applied to BR biosynthesis mutants to clarify the contributions of GA and BR. Overall, the data presented demonstrate interactions between GA and BR that vary widely throughout maize development highlighting the importance of assessing mutant phenotype contributions across multiple organs and developmental stages. Carolyn G. Rasmussen, 2016

7/2016 Yan He
Baldauf, JA et al. 2016. Plant Physiol 171:1144-1155
   Nonsyntenic genes drive tissue-specific dynamics of differential, nonadditive and allelic expression patterns in maize hybrids

Heterosis, or hybrid vigor, depicts the superior performance of heterozygous F1-hybrid progeny relative to the average of their homozygous parental inbred lines or the better performing parent. As a cross-pollinating plant, the F1-progeny display an exceptional heterosis. However, the molecular mechanisms determining the presence of heterosis are largely unclear. In this research, the authors investigated the performance of heterosis in maize primary root tissue, and found that the heterosis is reflected by differential, nonadditive and allelic transcriptome patterns. The number of differentially expressed genes between two parents is significantly beyond the comparisons of parent relative to hybrid. In addition, none of genes showed differentially expressed between reciprocal hybrids. Moreover, a large number of genes showed the alterations in nonadditive and allelic expression ratios in the comparison of parents versus hybrid, and two reciprocal hybrids. More importantly, the nonsyntenic genes relative to sorghum genome were highly overrepresented among those differential, nonadditive and allelic expression patterns compared to syntenic genes. This study highlights the importance of nonsyntenic genes in shaping the transcriptome landscape of hybrids to establish heterosis in the early developmental stage in maize root tissues. Yan He, 2016

7/2016 Michelle Facette
Ray, S et al. 2016. Plant Physiol 171:694-706
   Turnabout is fair play: Herbivory-induced plant chitinases excreted in fall armyworm frass suppress herbivore defenses in maize

Plants have multiple defense systems to address the multiple insults to their systems, including the salicylic acid (SA) pathway that promotes defense against biotrophic pathogens, and the jasmonic acid (JA) pathway that promotes defense against necrotrophic pathogens and herbivores. Previous work from the Luthe group showed that frass (excrement) from the fall armyworm suppresses maize host defense against herbivory by upregulating SA and associated genes and downregulating JA, thereby promoting armyworm feeding and growth. In this work, they identify some of the frass proteins active in this hijacking of maize defense. Fractionation of frass proteins and subsequent protein revealed the presence of several chitinases (including the known defense protein PR4) correlated with activation of SA genes that promote fall armyworm herbivory. Applying frass specifically depleted of chitinases eliminated this effect. Applying recombinant chitinases (instead of frass) to the plant also promoted fall army worm growth. This demonstrates how the fall army worm has taken advantage of the maize plant's own defense system to promote its own feeding and growth. Michelle Facette, 2016

7/2016 Eli Rodgers-Melnick
Wang, B et al. 2016. Nat Commun. pp. doi: 10.1038/ncomms11708
   Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

In any study of a complex genome, the specification of the transcriptome is an essential first step in the characterization of molecular systems. However, our ability to define a complete transcriptome is limited by the accuracy of gene prediction, the limitations of sequencing technology, the sampling of tissues, and our expectations of what a transcriptome should contain. In this study of the reference line B73, authors Bo Wang et al used PacBio sequencing to identify 111,151 unique transcripts from 6 tissues (root, tassel, ear, embryo, endosperm, pollen). This dataset covers approximately 70% of the maize RefGen_v3 filtered gene set, with an average of 6.5 isoforms per gene - a substantial increase over the 2.8 isoforms per gene in the RefGen_v3 dataset. Moreover, the number of isoforms is associated with cytosine methylation properties of the splicing junctions. The size distribution of the PacBio dataset also trends toward longer isoforms than the RefGen_v3 FGS. The authors find tissue-specific patterns of alternative splicing, though intron retention is dominant in all but the endosperm. They also discover a number of lncRNAs with tissue-specific properties, and they show that the epigenetic properties of lncRNA genes is similar to that of expressed protein coding genes. Interestingly, the authors were also able to discover and validate the presence of several trans-splicing events, in which the transcripts of distinct genes were spliced together at known splice junctions. The PacBio dataset is available through NCBI SRA under SRP067440. Eli Rodgers-Melnick, 2016

7/2016 Arnaud Ronceret
Huang, W; Du, Y; Zhao, X; Jin, W. 2016. BMC Plant Biology. 16:88
   B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)

The B chromosomes are additional dispensable chromosomes first reported in maize a century ago by Kuwada (1915). They usually don't affect plant growth. The work of Huang et al. used a leaf RNAseq transcriptome analysis of lines containing or not the B chromosome (B73, B73+1B, B73+6B). All the B-specific sequences are homologs of A chromosome but present few SNP or sequence distinctive features. Because it is difficult to distinguish if the sequences are coming from a B chromosome or a A homolog, they also compare an oat additional line containing a maize B chromosome (Starter without B and Starter +B). Their analysis show that there is very limited number of gene up-regulated (115) and even fewer genes down-regulated (15) in line containing B chromosome compared to line without B chromosome. The RNAseq analysis allowed to identify three B-specific LTR-containing expressed sequences. Two Gypsy elements: comp75688 (3250 bp in length), comp74447 (1,633 bp in length) and a Copia element: comp30393 (484 bp in length). qRT-PCR showed that comp75688 was expressed in a B-dosage dependent manner. Four B chromosome specific genes were also analyzed in detail (GRMZM2G013761B, GRMZM2G356718B, AF466202.2_FG007B and GRMZM2G356653B named after their closest A-chromosome homologs respectively located on chromosome 4, 1, 10 and 1). The B chromosome localization of these elements was confirmed by FISH experiments. These analysis suggest that the origin of the maize B chromosome is a mosaic of elements from different A chromosomes. Arnaud Ronceret, 2016

6/2016 Eli Rodgers-Melnick
Bartlett, ME, et al. 2016. Molecular Biology and Evolution. 33:1486-501
   Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions

The determination of floral organ identity is often used as the textbook example of developmental regulation in plants. Organ identity within the fluorescence is specified by the combinatorial action of MADS-box transcription factors acting according to the rules specified by the ABC(E) model of floral development. Petal and stamen development are directed by the B-class TFs, APETALA3 (AP3) and PISTILLATA (PI). Though obligate AP3/PI heterodimerization appeared early in angiosperm evolution, PI homodimerization has evolved independently several times in monocot and dicot lineages, indicating the protein-protein interactions of these critical TFs are relatively labile. In this study, authors Bartlett et al characterize the dimerization patterns of PI, the amino acid residues controlling PPI specificity, and their phenotypic effects of the PPI regimen on floral development in Arabidopsis thaliana. The grasses have two clades of the PI TFs - PI-1 and PI-2 - from an ancestral duplication. While most TFs in the PI-2 clade have the capacity for homodimerization, the maize ortholog, STS1, exists as an obligate heterodimer with its AP3 counterpart, SI1. The authors use domain swaps and site-directed mutagenesis to pinpoint a glycine (G) to aspartic acid (D) substitution at position 81 of STS1 that is sufficient to recapitulate homodimerization. Interestingly, examination of the maize HapMap2 data showed that the G allele was fixed in all the maize lines, segregating in the teosintes, and absent in the single sequenced tripsacum. Thus, fixation of STS1 obligate heterodimerization appears to be concomitant with maize domestication. Moreover, several residues with evidence of positive selection within the PI-2 clade coincided with probable PPI interfaces, based on alignment with orthologous protein structures. Eli Rodgers-Melnick, 2016

6/2016 Michelle Facette
Egger, RL; Walbot, V. 2016. Dev Biol doi: 10.1016/j.ydbio.2016.03.016
   A framework for evaluating developmental defects at the cellular level: An example from ten maize anther mutants using morphological and molecular data

Anther development includes a series of mitoses and cell fate specifications and followed by a transition to meioses that produce the male gamete (pollen). Eggers and Walbot use a series of analyses to characterize ten maize mutants defective in pre-meiotic, somatic development within the anther, and present a model for anther development. Mitotic divisions in the anther include periclinal divisions yielding new cell layers (and cell types) and anticlinal proliferative divisions. In each mutant, total number of anther cells and number of supernumerary cells arising from incorrect periclinal divisions was counted at different anther lengths (i.e., developmental stage). Using these data, the mutants were classified into three classes: two mutants had anticlinal proliferation defects but no periclinal division defects and no supernumerary cells; four mutants had periclinal division defects, resulting in additional cell layes and abnormal anther lobe cell numbers; and another 4 mutants periclinal division defects yet normal anther lobe cell numbers. Within each of these 3 classes, distinct mutant phenotypes (such as which cell layer ectopically divides or when it divides) were identified. Transcriptomic comparisons of 3 mutants (all of which fall in to the third class with periclinal division defects but normal anther numbers) vs their wild type siblings were performed. Although certain groups of genes were similarly altered in the three mutants, they each had a unique complement of down or upregulated genes. The framework presented here, most notably the careful spatio-temporal analysis of cell division, provides hypotheses for when each of these genes is acting during the coordinated process of the somatic phase of anther development. It will surely paly important future roles in understanding plant cell division and cell fate determination as well as understanding male germline development in maize. Michelle Facette, 2016

6/2016 Yan He
Carolyn Rasmussen
Je, BI et al. 2016. Nature Genetics 48:785-791
   Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits

Je et al. discovered that FASCIATED EAR3 leucine rich repeat receptor like kinase protein inhibits the proliferation of stem cells by responding to a CLAVATA3-like peptide (ZmFCP1) which is made in nearby differentiating cells. The fea3 mutant overproliferates cells in the shoot apical meristem, tassel and ear meristems which leads to a fasciated ear and thick tassel phenotype but little overall growth defect. Je et al. showed that FEA3 localizes in the central region of meristems, and then searched for the putative ligand of FEA3. They identified a peptide ZmFCP1, which is a CLAVATA3 like peptide, that reduced wild-type but not fea3 mutant root or shoot apical meristem growth. Consistent with the hypothesis that ZmFCP1 is the FEA3 ligand, the Zmfcp1 mutant had large shoot apical meristems and fasciated ears and overexpression of ZmFCP1 led to a reduction in shoot apical meristem size. ZmFCP1 was not expressed in the shoot apical meristem, but instead in nearby cells and the leaf primordia. Interestingly, they demonstrate that this feedback loop is conserved also in dicots: Arabidopsis thaliana fea3 mutants were fasciated and had large shoot apical meristems and CLE27 was identified as the putative ligand. The authors show that weak fea3 alleles increased kernel number and ear weight in hybrids suggesting a potential use in crop improvement. Together, Je et al. identified a conserved feedback loop where the peptide ZmFCP1 expression originates in organ primordia to control nearby stem cell proliferation through the FEA3 receptor. Carolyn G. Rasmussen, 2016

Shoot apical meristems are stem cells occurring in niches, which balance proliferation with the incorporation of daughter cells into organ primordial. This balance is assured by a feedback signaling pathway including CLAVATA (CLV) and WUSCHEL (WUS). Although such feedback systems are well described in animals and plants, it is not known whether and how signals provide feedback signals from organ primordial to control the stem cell niches. In this study, the authors cloned the gene (GRMZM2G166524) underlying the maize FASCIATEM EAR3 (FEA3) mutant, and it encodes a leucine-rich-repeat receptor which functions in stem cell control and respond to CLE peptide expressed in organ primordial. The authors propose a model suggesting that this new CLE signal moves from the organ primordial to the SAM, where it is perceived by FEA3 to restrict stem cell proliferation. Yan He, 2016

6/2016 Andrea L. Eveland
Rodgers-Melnick, E; Vera, DL; Bass, HW; Buckler, E. 2016. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1525244113
   Open chromatin reveals the functional maize genome

In this study, Rodgers-Melnick et al. profiled genome-wide chromatin accessibility in maize by analyzing differential sensitivity to micrococcal nuclease (MNase) digestion followed by high-throughput sequencing (DNS-seq). Their approach took advantage of relative sensitivity of chromatin to heavy and light concentrations of MNase to resolve regions of nucleosome occupancy and open chromatin from maize shoot and root tissues. MNase hypersensitive sites (HS) were identified as having significant DNS to heavy and light concentrations of MNase and were associated with potential occupancy of transcription factors and other regulatory machinery. For example, these regions were clearly associated with active promoter regions just upstream of transcriptional start sites and could be used, in most cases, as robust indicators of gene expression. They also showed that MNase HS marked known QTL in nongenic regions of the genome and can be used to resolve locations of distal enhancers of gene expression, e.g. the enhancer of tb1. The authors also showed that open chromatin regions were strongly associated with DNA hypomethylation and recombination hotspots. By projecting GWAS hits onto the open chromatin maps, they found 2-fold SNP enrichment within 2 kb of MNase HS sites compared to the space outside of these regions. Remarkably, while HS regions accounted for less than 1% of the genome, they explained ~40% of the heritable phenotypic variation in maize. Interestingly, the authors also showed that MNase HS regions are also significantly associated with GC-biased gene conversion, a nonadaptive selective force with potential implications for maize genetic load as well as heterosis. Rodgers-Melnick et al. demonstrate the far-reaching applications of DNS-seq in maize for defining regions of the genome that contribute to quantitative trait variation, which has enormous impacts on genome-assisted breeding and crop improvement. Datasets from this publication are available via the NCBI SRA (accession no. SRA302258). Andrea Eveland, 2016

6/2016 Arnaud Ronceret
Wolfgruber, TK et al. 2016. Frontiers Plant Sci 7:308
   High quality maize centromere 10 sequence reveals evidence of frequent recombination events

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5/2016 Carolyn Rasmussen
Kelliher, T, et al. 2016. Frontiers Plant Sci. 0:doi: 10.3389/fpls.2016.00414
   Maternal haploids are preferentially induced by CENH3-tailswap transgenic complementation in maize

In this paper, the authors demonstrate that using an engineered histone specific for centromeres, CENH3, allows efficient production of doubled haploids. Doubled haploids make rapid homozygous lines that are useful for industry and research. The engineered lines perform a little less than half as well (3.6% at best) as other haploid inducing maize lines (8-15%). First, they isolated a mutant in the ZmCENH3 gene (GRMZM2G158526) from the uniform Mu collection and also used RNAi to knock down expression. Next, two CENH3 variants were added back to theZmCENH3 mutants: one with a fluorescent protein fused to the full length protein, and one that replaced the CENH3 N-terminal tail with the standard Histone H3 tail from GRMZM2G158526. The CENH3 variant with the H3 tail has been used in other organisms to promote doubled haploids. Unfortunately, the strongest haploid inducer lines, which contained the CENH3 with the H3 tail, had variable results in multiple crosses. This variability potentially reflects the mixed background and raises the possibility of genetic modifiers of haploid induction within the lines (which contained both W22 and NP2222). Overall, this paper provides insight into improving the efficiency of doubled haploid inducers in maize. Carolyn G. Rasmussen, 2016

5/2016 Michelle Facette
Egger, RL; Walbot, V. 2016. Dev Biol doi: 10.1016/j.ydbio.2016.03.016
   A framework for evaluating developmental defects at the cellular level: An example from ten maize anther mutants using morphological and molecular data

Anther development includes a series of mitoses and cell fate specifications and followed by a transition to meioses that produce the male gamete (pollen). Eggers and Walbot use a series of analyses to characterize ten maize mutants defective in pre-meiotic, somatic development within the anther, and present a model for anther development. Mitotic divisions in the anther include periclinal divisions yielding new cell layers (and cell types) and anticlinal proliferative divisions. In each mutant, total number of anther cells and number of supernumerary cells arising from incorrect periclinal divisions was counted at different anther lengths (i.e., developmental stage). Using these data, the mutants were classified into three classes: two mutants had anticlinal proliferation defects but no periclinal division defects and no supernumerary cells; four mutants had periclinal division defects, resulting in additional cell layes and abnormal anther lobe cell numbers; and another 4 mutants periclinal division defects yet normal anther lobe cell numbers. Within each of these 3 classes, distinct mutant phenotypes (such as which cell layer ectopically divides or when it divides) were identified. Transcriptomic comparisons of 3 mutants (all of which fall in to the third class with periclinal division defects but normal anther numbers) vs their wild type siblings were performed. Although certain groups of genes were similarly altered in the three mutants, they each had a unique complement of down or upregulated genes. The framework presented here, most notably the careful spatio-temporal analysis of cell division, provides hypotheses for when each of these genes is acting during the coordinated process of the somatic phase of anther development. It will surely paly important future roles in understanding plant cell division and cell fate determination as well as understanding male germline development in maize. Michelle Facette, 2016

5/2016 Eli Rodgers-Melnick
Orozco-Ramirez, Q et al. 2016. Heredity 116:477-484
   Maize diversity associated with social origin and environmental variation in Southern Mexico

While many studies of plant evolution focus on genetic differentiation with respect to environmental adaptation, patterns of population structure among domesticated species also reflect their cultural heritage. Yet, few researchers have analyzed the interplay of cultural and non-anthropogenic environmental forces on a local scale. In this study, Orozco-Ramirez and colleagues characterize genetic and morphological differentiation of maize landraces in neighboring municipalities of disparate ethnicities within Southern Mexico. Each muncipality contains both mid and low-elevation regions, allowing partitioning of variance between anthropogenic and non-anthropogenic features. Morphological traits have little structure across the region, although they are differentiated slightly more according to municipality than according to elevation. The effects of differentiation due to sociological forces becomes clearer after examination of genetic data. Estimates of genetic differentiation from both STUCTURE and AMOVA show significant differentiation between municipalities but not between elevations within municipalities. Furthermore, the differentiation of putative maize races receives little support from the genetic data. Thus, while the effect of elevation on population differentiation is well-supported species-wide, cultural forces can have an even stronger impact on gene-flow at local scales. Eli Rodgers-Melnick, 2016

5/2016 Arnaud Ronceret
Hu, HX, et al. 2016. Genetics. 202:1267-1276
   The genetic basis of haploid induction in maize identified with a novel genome-wide association method

Haploid induction (HI) is a method now widely used to initiate the production of double haploids allowing the production of inbred lines in 1-2 generations. The actual diverse haploid lines derives more or less indirectly from the original haploid inducer "stock 6" described by Ed Coe in 1959. The history of haploid inducers development is retraced in Supplemental File S1 and their pedigree tree and relationships in File S2 and Figure 1. In order to find the genetic basis of HI, the authors developed an elegant new GWAS method called conditional haplotype extension (CHE) taking into account that the cases (inducers lines) are related to each other because they shear a common ancestor. Using the CHE approach using the data of an Illumina Maize SNP 50k bead chip they detect a common segment of 1 Mb on chromosome 1 found in the 53 inducers analyzed but not in 1482 non inducers lines. This region correspond to a previously QTL required for HI (qhir) found in different analyses on Bin1.04. This region was refined into two closely linked genomic segments named qhir11 (0.54Mb) containing a previously fine mapped (223kb) QTL for HI and qhir12 (3.97Mb). qhir11 was not diagnostic for differentiating inducers from non inducers while qhir12 shows a complete correlation. The resequencing of the inducer line CAU5 compared to non inducers allowed to identify a list of variants in 44 genes of the qhir11 region (File S5). From this list, the authors identified three genes candidates, two encoding a DNA binding protein (ZM01G18090 / GRMZM2G137502, a Dof zinc finger protein and ZM01G18020 / GRMZM2G135834, an ortholog of AtDEK3) and one encoding an ortholog of the ACR4 receptor kinase (ZM01G18110 / GRMZM2G096682). Further functional characterization of these genes will be needed to know whether the corresponding variants found in CAU5 can trigger HI in maize. This new GWAS / CHE method promises to be of interest to characterize historical mutants already introgressed in different backgrounds. Arnaud Ronceret, 2016

5/2016 Yan He
Li, YX, et al. 2016. Plant J. 86:391-402
   Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population

Flowing time is one of the major traits during maize domestication to facilitate the broad adaption from tropic to subtropical areas across the world. ZmCCT and VGT1, two genes principally attribute to the adaption of the flowering time have been identified. However, the former studies have also shown that the genetic components regulating flowering time in maize are linking to more than 40 genes. To comprehensive dissect maize flowering time variant, the flowering time traits were examined in an extremely large multi-genetic population, including two NAM panels and a natural association panel. By combining linkage and association analysis, a total of 90 flowering time loci were identified, which are either common or unique in different population backgrounds. The GWAS analysis demonstrated that about one thousand SPNs associated with flowering time and most of these SNPs distributed around 220 genic regions. These candidate genes provide a large repertoire of targets for further functional studies to interpret the molecular mechanisms in regulating maize flowering time. Yan He, 2016

Lists out the China Nested Association (CN NAM) panel.

5/2016 Andrea L. Eveland
Qiao, Z, et al. 2016. PLoS Genetics. 12:e1005991
   ZmMADS47 regulates zein gene transcription through interaction with opaque2

In this study, Qiao et al. characterized the interaction between OPAQUE2 (O2), a classic bZIP transcription factor (TF) that regulates zein protein biosynthesis in developing maize kernels, and a MADS box TF that has high sequence similarity to OsMADS47, which was thus named ZmMADS47 (ZmMADS47 = GRMZM2G059102 v3 coordinates = 1:17964695-17986258;GenBank: ACG34827.1). The protein-protein interaction between these two TFs was previously identified in a yeast-2-hybrid screen (Zhang et al., 2012). Here, the authors confirmed this interaction in vitro as well as in vivo by co-IP; the latter suggested ZmMADS47 and O2 exist in a complex of ~550 kD in maize kernels 15 Days After Pollination (DAP). In the endosperm of developing kernels, ZmMADS47 expression peaked at 15 DAP, while o2 expression was detected at 12 DAP and peaked at 20 DAP. To further characterize the function of ZmMADS47, RNAi lines were generated that knocked down its expression in maize. RNAseq-based transcript profiling of 15 DAP kernels between the RNAi knockdown lines and non-transgenic controls identified 1,071 differentially expressed genes, including those involved in "nutrient reservoir activity" such as a number of 19-kD and 22-kD α-zeins and the 50-kD γ-zein (data from RNA-seq experiment available from GEO: GSE70609). The authors used an EMSA assay to further show that ZmMADS47 binds directly to promoters of affects zein genes via a CATGT motif and that mutations in any one of the five bases of this core motif abolished binding ability. Interestingly, this motif is present in previously identified O2 binding motifs. Through a series of additional experiments, the authors described a model where ZmMADS47 cannot activate expression of zein genes on its own, but can enhance the activation of zein genes by O2. Previous ChIP-seq analyses for O2 (Li et al., 2015; RNAseq: GSE61830; ChIPseq data: GSE63991) indicated that not all O2 zein targets are co-bound and co-regulated by ZmMADS47 and that zeins targeted by O2 show various gene expression responses in the o2 mutant, suggesting there are additional transcriptional regulators of zeins that have yet to be discovered. Andrea Eveland, 2016

4/2016 Arnaud Ronceret
Sailer, C et al. 2016. Curr Microbiol 26:331-337
   Apomixis allows the transgenerational fixation of phenotypes in hybrid plants

In order to continue feeding the planet with a world population expected to reach 9 billion people by 2050, agriculture need a second green revolution. It has long been expected that introducing apomixis in crop plants could be a solution to this major agronomic issue. Apomixis allows plants to reproduce by seeds containing a clonal progeny. In theory, apomixis could allow to propagate the hybrid vigor (heterosis) because it can propagate the genotype. However empirically it was not proved that such a strategy could work because of potential interferences between the poorly understood processes of apomixis and heterosis and/or trans-generational epigenetic effects. The study of the group of Ueli Grossniklaus now shows for the first time that the use of an apomictic reproduction allows to propagate the benefits of heterosis. The plant model used is a similar natural apomictic hawkweed (Hieracium pilosella) that confused Gregor Mendel 150 years ago. The study elegantly check if 11 F1 hybrid selected to reproduce clonally keep 20 agronomic relevant vegetative and reproductive phenotypes using appropriate statistical tests. Only one apomictic line out of the 11 show instability. The maintenance of the heterotic effect is observed in 90% of the case (18 of the 20 traits examined) during 2 apomicitc generations. The 2 traits that show instability through generations (age at flowering and number of leaves at bolting) are traits related to flowering known to be largely epigenetically influenced. This study is a proof of concept that the old idea of using apomixis for hybrid propagation has sound grounds and could be applied in crops. This analysis is a green signal to invent apomictic strategies to revolutionize maize production in the years to come. Arnaud Ronceret, 2016

4/2016 Michelle Facette
Majeran, W et al. 2008. Molecular & Cellular Proteomics 7:1609-1638
   Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells

There are currently no comments for this article.

3/2016 Arnaud Ronceret
Feng, C, et al. 2016. Journal of Genetics and Genomics. 43:37-43
   Efficient targeted genome modification in maize using CRISPR/Cas9 system

Feng et al. describe the use of the targeted genome modification method of 'Clustered regularly interspaced short palindromic repeats' (CRISPR)/Cas9 system in maize. Considering the interest of this new technique for the maize genome manipulation (see the article of Zhu et al. 2015 reviewed by Eli Rodgers-Melnick in 2/2016) the authors address two essential issues for the use of this technology. First the efficiency of the system was analyzed by the effect of a construct whose single guide RNA (sgRNA) was designed to target the 8thexon of the zebra7 / lemon white1 (Zmzb7 = GRMZM2G027059/ ZM01G51760) gene, the unique ortholog of the Arabidopsis Chloroplast Biogenesis 6 (CLB6 = AT4G34350) gene. The authors found several deletions in the targeted site and rapidly recovered an expected albino plant due to the production of two mutated alleles leading to the loss of function of the Zmzb7 gene. The relatively high ratio of mutants obtained was rationalized by checking the efficiency of their construct on transformed maize protoplasts. By analyzing indels in the targeted loci from the protoplast genomic DNA the authors were confident they could use their construct for the transformation and regeneration of mutated calli and plants. Their second important contribution was to show that it is possible to mutate not only euchromatic loci but also genes located in maize centromeric and pericentromeric regions. Targeted mutations in 5 (Hsg3 = GRMZM2G332562 / ZM05G22190 and Hsg4 = GRMZM2G080129 /ZM05G22230 on chromosome 5, Hsg12 = GRMZM2G438243 / ZM02G19480, Hsg6 = GRMZM2G170586 / ZM02G19610 and Hsg7 = GRMZM2G099580 / ZM02G19660 on chromosome 2) of the 12 tested heterochromatic located loci were efficiently obtained. In addition the efficiency of the mutagenesis was independent of the expression of the targeted loci. The authors have also evaluated the specificity of their constructs and found no off-target mutations if the PAM (protospacer adjacent motif) had more than 3 different base pair. This analysis shows that the CRISPR/Cas9 targeted mutagenesis system is not only highly specific but is efficient in euchromatic and heterochromatic regions of maize. Arnaud Ronceret, 2016

The authors targets 12 genes located in maize centromeric or pericentromeric heterochromatin. The 5 successfully mutated gene are listed in the Ed Board member comment. The 6 unsuccessful target gene models were: GRMZM2G091313, GRMZM2G083935, GRMZM2G170577, GRMZM2G000411, GRMZM2G429781, GRMZM2G342426, and the single undetermined target was GRMZM2G135228

3/2016 Andrea L. Eveland
Yang, H et al. 2016. Plant Cell pp.doi: 10.1105/tpc.15.00691
   Genome-wide mapping of targets of maize histone deacetylase HDA101 reveals its function and regulatory mechanism during seed development

In this study, Yang et al. explored the role of the maize histone deacetylase, HDA101, in kernel development. Histone deacetylases (HDACs) remove acetyl groups from lysine residues of acetylated histones, typically leading to tight, inaccessible chromatin structure. In maize, the HDAC HDA101 influences several aspects of development, including kernel size. Proper kernel development relies on differentiation of key endosperm cell types early in development (~4-6 DAP; Days After Pollination) including the endosperm transfer layer (BETL), which functions in nutrient uptake from maternal tissue to the endosperm. Overexpression (OX) of HDA101 leads to smaller kernels, which is due, at least in part, to defects in transfer cell development. The authors showed that a significant number of BETL marker genes were mis-expressed in hda101 OX mutants, both in expression level and in spatiotemporal pattern. In normal, B73 developing kernels, HDA101 protein begins to accumulate ~3DAP, however, in hda101 OX mutant kernels, protein accumulation is delayed until later stages of development where it accumulates at higher levels compared with normal kernels. To determine the genetic mechanisms of HDA101 during early kernel development, the authors mapped genome-wide occupancy of HDA101 using an HDA101-specific antibody. ChIP-seq was performed with two biological replicates using 4DAP kernels from normal B73 plants. The hda101 OX mutant line was used as a negative control. In total, ~10k peaks were identified as putative binding sites, including ~7.5k corresponding to protein-coding genes. BETL-specific genes were not among these putative targets, suggesting indirect regulation of these genes. Similar to what has been shown for mammalian HDACs, HDA101 primarily targets genes with high and intermediate expression levels and here, binding tends to be enriched in TSSs. This is surprising given that HDACs are generally considered repressors of gene expression. The authors also showed a global increase in histone acetylation at 4DAP resulting from loss of HDA101 protein in the hda101 OX lines. They further performed ChIP-seq for histone H4 lysine (H4K5ac) in normal B73 and hda101 OX kernels at 4DAP and showed hyper-acetylation at H4K5ac in ~1/3 of HDA101 direct targets in hda101 OX lines, but this did not seem to alter transcript levels. Interestingly, a small subset of inactive genes that are negatively regulated during kernel development was also targeted by HDA101. Loss of HDA101 binding led to hyper-acetylation and expression of these genes, suggesting a mechanism by which HDA101 controls endosperm differentiation. Co-IP experiments also showed that HDA101 interacts with members of various chromatin remodeling complexes and co-repressors. Taken together, this work highlights a role for chromatin-related mechanisms in regulation of kernel size. Andrea Eveland, 2016

3/2016 Carolyn Rasmussen
Jamann, TM et al. 2016. Theor Appl Genet 129:591-602
   A remorin gene is implicated in quantitative disease resistance in maize

The authors fine map a quantitative disease resistance locus to a maize remorin ZmREM6.3 (GRMZM2G107774) and demonstrate that a Uniform Mu remorin mutants are more susceptible to Northern leaf blight fungal infection. This quantitative disease resistance locus, located on the short arm of chromosome one, provides resistance to two fungi: Northern leaf blight (Setosphaeria turcica) and common rust (Puccinia sorghi) as well as the bacterial pathogen Pantoea stewartii that causes Stewart���s wilt. The Northern leaf blight locus was narrowed to a 243 kb region containing several candidate genes. Combining mutant and expression analysis allowed them to identify remorin as a protein conferring disease resistance: mutants were more susceptible to northern leaf blight. Remorin proteins are plant specific phosphoproteins that localize to membrane microdomains and have characterized roles in symbiosis and viral movement. Together, the authors used a variety of tools to identify genes required for quantitative disease resistance locus and finally showed that remorin ZmREM6.3 plays a role in fungal disease resistance. Carolyn G. Rasmussen, 2016

3/2016 Yan He
Li, C; Shen, Y; Meeley, RB; McCarty, DR; Tan, BC. 2015. Plant J. 84:785-799
   Embryo defective 14 encodes a plastid-targeted cGTPase essential for embryogenesis in maize

Embryogenesis is a complex process involving coordinated expression of thousands of genes with diverse functions. The embryo defective 14 (emb14) mutants represent a unique class of mutants with defective embryogenesis but endosperm develops normally. In this study, the authors map-cloned a maize emb14 mutant by transposon tagging, and concluded that Emb14 gene encodes a circular permuted, YqeH class GTPase protein, which putatively function in 30S ribosome formation in plastids. The cytological analysis identified that loss of Emb14 function causes arrested embryogenesis at the early transition stages. Emb14 protein is localized in chloroplasts and has GTPase activity showed by in vitro assay. Emb14 is constitutively expressed and highly abundant in transition stage of embryogenesis. The disruption of Emb14 results in severe reduction in the accumulation of 16S rRNA and plastid. In sum, this study demonstrates that EMB14 mutant is caused by the mutation in a GTPase gene, which is shown to be essential for embryogenesis in maize. Yan He 2016

3/2016 Eli Rodgers-Melnick
Bousios, A et al. 2015. Genome Res 26:226-237
   A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

Approximately 80% of the maize genome consists of transposable elements (TEs), many of which remain capable of active transposition. Therefore, the suppression of TE-mediated mutagenesis is a ubiquitous feature of the maize regulatory landscape. In this study, authors Bousios et al characterize the targeting of siRNAs to the Sirevirus LTR genus of retrotransposons, which together comprise approximately 20% of the maize genome. After identifying 13,833 full length Sirevirus TEs, the authors examine the mapping of leaf, tassel, and immature ear siRNA libraries to the B73 reference genome. Although 21-nt, 22-nt, and 24-nt siRNAs map to locations spanning the LTRs and internal (INT) domains of all Sirevirus families, the authors discover consistent siRNA hotspots corresponding to palindromic sequences within cis-regulatory regions of the LTRs. Despite the common hotspot characteristics, members of separate families largely lack shared siRNAs. The authors also demonstrate that transcripts including the palindromic regions can form hairpin RNAs, which may provide a basis for the generation of siRNAs from primary transcripts. Interestingly, the authors observe a mixed relationship between the age of the Sirevirus TEs and the numbers of siRNAs targeting them. Although an average negative relationship exists between TE age and siRNA targeting density, very old elements tend to be targeted as heavily as very young elements - with siRNAs clustered around intact palindromic hotspots. The evolutionary basis for the apparent conservation of these LTR palindromic sequences in very old TEs is currently unclear, but future investigation may shed considerable light on the evolutionary dynamics and regulatory mechanisms involved in TE control. Eli Rodgers 2016

3/2016 Michelle Facette
Johnston, R et al. 2015. New Phytol 205:306-315
   Ontogeny of the sheathing leaf base in maize (Zea mays)

Johnston et al. use several microscopic techniques to describe leaf initiation in maize. Their detailed descriptions of leaves as they emerge from the meristem confirms and clarifies fundamental differences between monocot and dicot leaf emergence, and using these data they form a model describing the patterning of the sheathing leaf base and parallel venation found in monocots. Firstly, they use computed tomography (CT) imaging of leaves as they emerge. Their 3D analyses show that new sheath margins (but not blade margins) overlap from outset in plastochron 3, sheathing the shoot apex from emergence. They follow their CT analysis by using PIN1a-YFP and DR5-RFP expressing plants as well as a PIN1 antibody to determine the pattern of auxin transport within leaf founder cells. Finally, they use in situ localization to determine the expression of genes known to be involved in auxin biosynthesis and leaf patterning. Specifically, they determined the expression domains of the auxin biosynthesis gene SPARSE INFLORESCENCE1 (SP1); AUXIN RESPONSE FACTOR3a (ARF3a); the HD-ZIP transcription factors ROLLED1 (RLD1) and PHABULOSA1 (PHB1); and maize orthologs of the A. thaliana organ boundary gene CUP-SHAPED COTELYDON (CUC). These in situ analyses together with the PIN1 and DR5 localization data illustrate that auxin maxima occurs around the circumference of the shoot apex (as opposed to a localized bump in dicots). These maxima then lead to provascular strands and eventually parallel venation. These detailed analyses provide a model for fundamental aspects of monocot leaf development. Michelle Facette, 2016

2/2016 Andrea L. Eveland
Baute, J et al. 2016. Plant Physiol pp.doi: 10.1104/pp.15.01883
   Combined large-scale phenotyping and transcriptomics in maize reveals a robust growth regulatory network

In this study, Baute et al. performed an integrated analysis of in-depth phenotyping of 197 maize recombinant inbred lines (RILs) belonging to two different segregating populations, and their correlation with tissue-specific transcript profiles, to resolve gene expression signatures contributing to leaf biomass traits. This work extends the authors' previous analysis of a B73xH99 bi-parental mapping population to now incorporate a MAGIC (multiparent advanced generation intercross) 8-way RIL population. Ten parameters related to leaf size traits were measured in the 197 RILs including leaf length, width, area and weight, 5 measures of growth rate kinetics, and size of the cell division zone (DZ). In addition, fresh and dry weight was measured at the seedling stage. In general, correlations (PCC) between traits tended to be stronger in the MAGIC population, likely due to more phenotype variation. Positive correlations between DZ size and leaf size traits suggest that the number of dividing cells is potentially a key factor in determining final organ size. Therefore, the authors tested transcriptional differences between the 197 genotypes by performing RNA-seq on the proliferative DZ tissue. They determined linear transcript-phenotype correlations for each of the traits in both populations separately and for each trait, selected the top 1% most correlated and most anti-correlated genes. This resulted in 226 genes that were correlated or anti-correlated with at least one trait in both populations. Annotation of this gene set revealed that functional processes related to "regulation of transcription", "protein synthesis" and "cell wall synthesis and degradation" were highly enriched. Of the 56 transcription factors identified in this gene set, many were related to hormone regulation, leaf architecture and chromatin structure, and tended to be robustly correlated with leaf size. A number of the 226 genes had previously been implicated in leaf size and growth processes, however the majority had not and 48 genes were of unknown function. To narrow these candidates, the authors performed network analysis by integrating publically available expression resources for maize and protein-protein interaction data leveraged from Arabidopsis. A highly-connected growth regulatory network of 185 genes and 943 edges was established and revealed sub-networks of candidate genes co-expressed with known regulators of organ growth and final size. Results from this work provide a high-resolution resource of co-expressed candidate genes related to leaf size and growth rate, which can potentially be leveraged for increased biomass in crop improvement programs. Andrea Eveland, 2016

2/2016 Michelle Facette
Thatcher, SR et al. 2016. Plant Physiol 170:586-599
   Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

In this paper, Thatcher et al., use RNA-seq to systematically examine different splice isoforms in the B73 inbred line in different tissues and under well-watered and drought conditions. After filtering out low abundance transcripts or those that were not in multiple biological replicates, they identified more than forty-eight thousand novel transcripts. They used Principal Components Analysis to determine that (based on the % relative abundance of a splice isoform) different tissue types and developmental stages separated more clearly than did drought and well-watered conditions of the same tissue. They further analyzed the types of transcript isoforms. Interestingly, the proportion of isoform variations caused by intron donor/acceptor changes was stable across tissues, while exon skipping was rare in most tissues but occurred more commonly in developing ears. This demonstrating that certain splice variants are under developmental control. Using established rules from the literature, they also analyzed whether certain splicing isoforms would undergo relative increases or decreases in nonsense-mediated decay. While many isoforms resulted in a predicted increase or decrease in nonsense mediated decay, no particular tissue experienced more (or less) nonsense mediated decay than other tissues. They then proceeded to examine specific examples of changes in transcript isoform abundance, drawing examples from changes across embryo, endosperm vs seed development or well-watered vs drought conditions. This included a variety of examples such as those that result in different protein isoforms or those that result in alternate C-terminal untranslated tails, potentially resulting in differences in nonsense mediated decay. They conclude the paper by showing that across different tissues, there was a positive correlation between the expression of splicing-associated genes and the number of genes undergoing alternative splicing, suggesting that expression of these splice factors contribute to alternative splicing, and that it is indeed a developmentally controlled process. They further give an example of a particular splicing factor whose expression correlates well across drought and well-watered conditions, hypothesizing that it may play a role in alterative splicing during drought. Together, the paper gathers a large amount of data of alternative splice isoforms in maize and lends evidence towards developmental and environmental splice-specific changes. Michelle Facette, 2016

2/2016 Yan He
Pan, Q et al. 2015. New Phytol pp.doi: 10.1111/nph.13810
   Genome-wide recombination dynamics are associated with phenotypic variation in maize

Meiotic recombination is the most important source of genetic variations in higher eukaryotes. Recently the genome-wide distribution of recombination has been mapped in Arabidopsis, rice and maize through large-scale population study. The results show that recombination is not uniformly distributed along chromosomes, while generally higher in chromosomal arm and lower in centromeric/pericentromeric regions. At a relative fine-scale, some regions showing much higher frequency of recombination is designated as recombination hotspots and the mechanism or genomic features underlying the appearance of hotspot emerge to be elucidated. In this research, recombination events were extensively surveyed in 12 maize segregation populations using high-resolution distribution of SNPs makers. The results showed substantial variations in the recombination frequency and distribution along maize chromosomes, which is consistent to several previous studies. Meanwhile, 143 recombination hotspots were identified, which locates in both intragenic regions and intergenic regions. Interestingly, the overall count of intragenic recombination events maintain invariable in a given population, and therefore, the variation of recombination between different populations mainly attribute to intergenic recombination. More importantly, the study found that the significant associations between intergenic recombination and variation in gene expression level as well as agronomic traits, pointing out that the intragenic recombination plays a role in plant phenotypic diversity. All these results provide novel insight into the association of recombination with gene expression and phenotypic variation, which will greatly enhance our understanding of recombination in maize evolution. Yan He, 2016

2/2016 Arnaud Ronceret
Oury, V et al. 2015. Plant Physiol pp.doi: 10.1104/pp.15.00268
   Ovary apical abortion under water deficit is caused by changes in sequential development of ovaries and in silk growth rate in maize

What is the effect of drought on ear seed-set in maize ? The cause of the typical ear devoid of fertilized kernel at its apex is now explained by extensive morpho-physiological analysis by Oury et al.. In water deficit conditions at the time of anthesis, grain abortion is observed, even when viable pollen is used for pollination. The authors followed for almost a month ovary volume and silk growth as a function of time and position on the ear in four hybrids under four levels of water deficit. The authors found that in water deficit conditions, silk growth rate decreased and stopped simultaneously for all ovary cohorts 2 to 3 days after first silk emergence, 5 days earlier than in well-watered plants. Abortion occurred in the youngest ovaries whose silks did not emerge 2 days before silk arrest. This mechanism allows production of at least few viable seeds under water deficit, but causes major yield loss. Its modelling may have important consequences for breeding drought tolerant maize. Arnaud Ronceret, 2016

2/2016 Carolyn Rasmussen
Lunardon, A; Forestan, C; Farinati, S; Axtell, MJ; Varotto, S. 2015. Plant Physiol. 0:DOI: 10.1104/pp.15.01205
   Genome-wide characterization of maize small RNA loci and their regulation in the required to maintain repression6-1 (rmr6-1) mutant and long-term abiotic stresses

The authors performed small RNA (sRNA) sequencing under well watered, drought and salinity conditions to identify differentially expressed sRNAs. Surprisingly few sRNAs were differentially expressed under drought and/or salinity conditions. To identify specific 24-nucleotide small interfering RNAs amplified by RNA polymerase IV, the authors compared small RNA generated in wild-type and a mutant in a subunit of RNA polymerase IV, the required to maintain repression 6 (rmr6) mutant. After sequencing small RNAs, they identified 48 MIRNA loci and ~250,000 non-MIRNA loci. New MIRNA loci, characterized by RMR6 independent accumulation of 21 and 22 nucleotide miRNAs, were identified: 3 from the miR166 family and 6 previously uncharacterized miRNA families. Several miRNAs were altered upon abiotic stress conditions: miR156 was induced by drought, while the phosphate homeostasis regulator miR399 was down regulated. Very few sRNA loci were altered, but five trans-acting short interfering TAS3 loci were down-regulated in drought-stressed plants, similar to previous observations. In general, differentially expressed genes under various conditions were not due to the loss of 24 nucleotide siRNAs in the rmr6 mutant, suggesting that siRNAs are not immediately necessary to maintain heterochromatic regions of the DNA. Carolyn G. Rasmussen, 2016

2/2016 Eli Rodgers-Melnick
Zhu, JJ et al. 2016. Journal of Genetics and Genomics 43:25-36
   Efficiency and inheritance of targeted mutagenesis in maize using CRISPR-Cas9

Although the promise of target-specific genomic edits has been within the grasp of plant geneticists since the advent of zinc finger nucleases (ZFNs), the previous ZFN and TALEN procedures require laborious and expensive protein engineering. The introduction of the CRISPR/Cas9 system has since enabled high-throughput, inexpensive edits to many species through the use of highly-configurable guide-RNAs (sgRNAs) for target sequence search. Previously published work on CRISPR/Cas9 editing in maize studied mutagenesis in stable T0 lines and following transient somatic cell transformation. In this study by authors Zhu et al, transformation efficiency, off-target effects, inheritance, and impacts on the global transcriptome are studied following transformation of maize protoplast with an Agrobacterium tumefaciens-delivered sgRNA-Cas9 expression vector. The authors discover approximately 2.4 million unique genic sgRNA targets within the B73 genome, which encompass over 95% of high-confidence protein coding genes. Over half of these target stites are contained within the first 2 coding exons, enabling targeted knock-outs of most maize genes. They take advantage of the qualitative phenotype induced following knockout of the PSY1 gene to profile both mutational efficiency and inheritance of mutations into the T1 generation. Of the 7/52 T0 lines positive for the Cas9 protein, mutation frequencies differed due to variation in the developmental stage where edits occurred. Indeed, while the seedling from one line was uniformly heterozygous for single mutant versions of both alleles, the other six lines contained a variety of edits to the target regions with mutational efficiencies between 65% and 87%. These numbers and the associated variegated phenotypes indicate that Cas9 continues to catalyze directed double-strand breaks throughout development. Yet, examination of computationally-identified regions of similarity to the targeted PSY1 region yielded no evidence of off-target effects. Moreover, self-fertilization and crosses to wild-type plants yielded the expected Mendelian inheritance patterns within kernels, with the corresponding seedling phenotypes, indicating that CRISPR/Cas9 edits are stably inherited by the T1 generation. Lastly, the lack of any significant expressional changes to the mutant transcriptome further substantiates the use of CRISPR/Cas9 for precise genetic experimentation in the highly complex and repeat-rich maize genome. Eli Rodgers-Melnick, 2016

1/2016 Michelle Facette
Vilela, B et al. 2015. Molecular Plant 8:709-721
   Casein kinase 2 negatively regulates abscisic acid-activated SnRK2s in the core abscisic acid-signaling module

Vilela et al. describe the phosphoregulation of the maize Snf-related kinase2 (SnRK2) ZmOST1. ZmOST1 orthologous to Arabidopsis OPEN STOMATA1, which is a key regulator of ABA signaling.OST1 kinase was previously thought to be regulated by autophosphorylation, but here the authors use biochemistry to demonstrate that Casein Kinase 2 (CK2) phosphorylates and regulates the stability of maize OST1, thereby adding another regulator to the ABA signaling module. Using in vitro kinase assays, they show that CK2 phosphorylates ZmOST1 within the "ABA-box" located in the C-terminus of the protein. Using transient assays in tobacco, they show that ZmOST1 normally accumulates in the nucleus cytosol, but when CK2 is co-expressed, OST1 localization shifts towards almost exclusive nuclear, and accumulates in nuclear speckles. Moreover, co-expression of OST1 and CK2 leads to eventual OST1 degradation, and this degradation is inhibited by the addition of MG132, implicating proteasome-degradation. This degradation is also dependent on the ABA-box. Moreover, phosphomimic mutations in OST1 at the site of CK2 phosphorylation increases the interaction with the PP2C ABI2, another core module of ABA receptor. Finally, transgenic maize lines overexpressing wildtype OST1 are hypersensitive to ABA; and transgenic lines overexpressing a phosphodead version of OST1 are even more hypersensitive to ABA. Together, the data suggest that CK2 phosphorylation negatively regulates ABA signaling by promoting proteasome-dependent degradation of OST1 kinase. This adds another key regulator to the ABA signaling pathway. Michelle Facette, 2016

1/2016 Eli Rodgers-Melnick
Leiboff, S et al. 2015. Nature Communications 6: 8974
   Genetic control of morphometric diversity in the maize shoot apical meristem

The shoot apical meristem (SAM) harbors the pool of stem cells that ultimately give rise to all the aboveground organs in plants. Accordingly, the SAM has been the target of numerous small-scale genetic studies in a variety of model species. However, despite elucidating the detailed genetic network underlying SAM development, mutational approaches do not necessarily illuminate the naturally-occurring genetic variation associated with differences in SAM morphology. In this study, Samuel Leiboff and colleagues characterize the morphology of the SAM in 369 diverse maize inbred lines using a simple parabolic model. They first demonstrate the predictive potential of microscopic SAM morphology by quantifying its correlation with adult quantitative traits, including flowering time, plant height, and stem diameter. The core of the study is then devoted to mapping the basis of natural SAM morphological differences using mixed model GWAS. Like many studies of traits putatively under high purifying selection, GWAS did not uncover any previously identified master regulators of SAM development. Nonetheless, the authors do identify 23 candidate genes, including genes with putative functions in hormone transport and cell division. They further functionally characterize the microscale physiological effects associated with alternative forms of associated SNPs. For instance, in situ transcript hybyridization demonstrates that a non synonymous mutation in the third exon of ZmLAX2, a predicted regulator of auxin influx, is associated with extension of its expressional domain into the SAM flank across from the incipient P0 leaf primordia. SNPs from two other candidate genes, ZmSDA1 and ZmBAK1, were found to be associated with increases in cell number and cell size, respectively, independent of variation in SAM volume. As the era of high-throughput phenomics and genomic prediction ramps up, the genetic dissection of seedling microscale traits and their relationships to yield components in adult tissues will likely rise to greater prominence. Time will tell whether such such microscopic variation will inform future crop growth models and methods for genomic prediction. Eli Rodgers-Melnick, 2016

1/2016 Carolyn Rasmussen
Sidhu, GK, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1514265112
   Recombination patterns in maize reveal limits to crossover homeostasis

The authors demonstrated that there is significant variability in the number of crossovers among different inbred lines, and further, that there is a strong correlation between amount of meiotic double strand breaks and crossing over events. This indicates that crossover homeostasis (where the number of crossover events is tightly regulated) is not the major driver of crossover number in maize. Double strain break number is strongly correlated with crossover number for both inbred lines and also for hybrids: the genetic distance between parents in hybrids did not increase the amount of crossovers. The minimum amount of crossing over, required for chromosome stability and increased genetic diversity, is one per homologous chromosome. The authors developed an elegant method combining chromosome spreading with three dimensional image reconstruction to assess the number of crossovers, which they used to measure crossing over events as well as chromosome pairing. One hypothesis based on data from non-plant organisms was that chromosome pairing and synapsis is associated with crossing-over, but this was not the case in maize: synaptonemal complex distances were similar in inbred lines with drastically different crossover number. A positive linear correlation was observed between double-strand breaks and crossing-over while a negative linear correlation was observed between crossover number and crossover interference. Overall, the authors propose that increasing the number of double strand breaks will lead to more recombination. Carolyn Rasmussen, 2016

1/2016 Andrea L. Eveland
Mejia-Guerra, MK, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00630
   Core promoter plasticity between maize tissues and genotypes contrasts with predominance of sharp transcription initiation sites

In this study, the authors present genome-wide maps of transcription start sites (TSSs) in maize using CAGE (cap analysis of gene expression). Their analyses, which included genotype- and tissue-specific TSS profiles, can be used to determine the location of core promoters in the maize genome and variation in promoter architecture contributing to cis-regulatory differences in gene expression. Each gene is typically characterized by multiple TSSs, which collectively make up a promoter cluster. Results from this study showed that the majority of maize promoter clusters display a sharp peak (in plots of TSS vs. genome position), similar to those in mice, yet different from Drosophila and Arabidopsis, where promoter clusters are predominantly broad. The authors speculate that this potential link between core promoter shape and genome size may reflect a mechanism for more focused transcriptional initiation in species with large, repetitive genomes, such as maize and mouse. In addition, a link between promoter shape and gene expression (both level and tissue-specificity) was observed based on publically available maize RNA-seq data. In general, genes associated with broad promoter clusters showed higher median expression levels than those with sharp promoters, however the most highly expressed genes tended to have sharp promoters. Approximately 38% of all maize genes harbor a TATA motif, which is enriched in sharp promoters. Other specific DNA motifs were also preferentially enriched in promoter clusters with either broad or sharp shapes. Comparative analysis of CAGE profiles between two tissues, roots and shoots of 14 day old seedlings, and from two divergent maize inbred lines, B73 and Mo17, revealed hundreds of instances of tissue- and haplotype-specific TSS occurrences. For 11 genes, shifts in the dominant TSS between B73 and Mo17 resulted in a new ATG. For most of these genes, indels were identified, suggesting genetic variation can generate alternative TSS. The authors chose a subset of genes with predicted alternate promoter usage and experimentally validated that they indeed generated diversity in protein size and localization. This study represents the first experimentally generated, genome-wide analysis of transcription initiation in maize. Results from this work provide a valuable resource for dissecting cis-regulatory architecture and gene regulation in maize, which will be critical as we move towards precision breeding and engineering for crop improvement. This resource also significantly improves annotation of the maize genome. Andrea Eveland, 2016

1/2016 Yan He
Qi, W et al. 2015. Plant Physiol 170:971-988
   Maize reas1 mutant stimulates ribosome use efficiency and triggers distinct transcriptional and translational responses

As a fundamental cellular process, ribosome biogenesis plays key roles in nearly all cycles of plant development. However, the cellular responses to impaired 60S ribosome biogenesis are not fully understood. In this paper, the authors found that, the reduced 60S ribosome biogenesis in a mutant called rea1-ref/dek, caused seed-lethality in maize via differentially regulating the transcription and translation of a large number of genes which are involved in translation efficiency and cell proliferation. Rea1 encode an AAA-ATPase, an enzyme controlling 60S ribosome export from the nucleus to the cytoplasm after ribosome maturation. The authors identified that in dek mutant, mature 60S ribosome subunits are decreased in the nucleus and cytoplasm, whereas accompanied with increased proportion of actively translating polyribosomes in cytosol. In addition, the authors found that the general translation efficiency was increased since phosphorylation of eIF2alpha was reduced but the eEF1alpha level was increased. Moreover, there is selective translational regulation of different groups of genes for intensive usage of quantitatively limited mature ribosome. All the above mentioned abnormalities inhibited cell proliferation, leading to slower growth and survival of maize seed development. This study provides more insight into cellular responses after impaired ribosome biogenesis. Yan He, 2015

1/2016 Arnaud Ronceret
Li, X et al. 2015. Nature Communications. pp.doi: 10.1038/ncomms7648
   Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

Analyzing meiotic recombination is of fundamental importance for understanding the dynamic of evolution of intraspecific genome diversity. Li et al. adapted for the first time in maize the classical toolkit of meiotic recombination studies using tetrad analysis. The sites of recombination can now be directly analyzed using high throughput sequencing of individual microspore coming from a single male meiosis. In order to trace recombination, two divergent genomes of the sequenced inbred parents Zheng58 and SK were used. The technique is based on micropipette isolation of male tetrads (the four microspores coming from a meiotic division) collected from immature meiotic tassels of two F1 (SK/Zheng58) plants. From an individual tetrad, each microspore containing an haploid recombined chromatid is isolated and analyzed at the whole genome sequence level thanks to single microspore genomic DNA amplification and sequencing by Illumina HiSeq. The sequencing of 96 chromatids from 24 tetrads lead to a high resolution mapping of 924 crossing overs (COs). The number of COs per male meiosis varies from 8 to 29 and seems distinct among the two individual plant analyzed. Most of the COs occurs in genes, and are mainly found in 5' and 3' UTR regions. The strength of interference was measured using coefficient of coincidence. Interestingly, it identifies a strong negative interference at the whole chromosome level, as in barley, but positive interference for COs closer to 10 Mb. In addition a weak chromatid interference phenomenon was also observed. This new technique open the possibilities to dissect in depth the recombination process in different hybrids, in different conditions as well as in meiotic mutants affecting recombination. It will be interesting to follow its more challenging development in female tetrad in order to understand at the whole genome level the distinct recombination rate and pattern of female meiosis. An associated detail protocol of this technique can be found at: Arnaud Ronceret, 2016

12/2015 Raffaella Battaglia
Bartlett, ME, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00679
   The maize PI/GLO ortholog zmm16/sterile tassel silky ear1 interacts with the zygomorphy and sex determination pathways in flower development

e functional characterization of the maize class B gene sterile tassel silky ear 1 (sts1) allows the Authors to describe conserved and divergent molecular mechanisms involved in floral organ differentiation and in the establishment of the zygomorphy program in maize flowers. Considering tassel florets, sts1 mutants show the homeotic conversion of the second and third whorls into lemnas/paleae-like structures while in ear florets the Authors describe the homeotic conversion of stamens to carpels. Positional cloning experiments indicate that the sts1 phenotype is due to a mutation in the B class gene Zmmm16, a maize PI/GLO ortholog. As expected, STS1 forms obligate heterodimers with the AP3/DEF orthologs that positively control class B genes expression. As other grass flowers, maize flowers have a single plane of symmetry; while the establishment of the zygomorphy program has been studied in species like A. majus; it is still not clear whether a conserved molecular program occurs in grass flowers. Interestingly, STS1 protein localization experiments, elegantly combined with visualization of auxin dynamics to follow organ initiation, reveal that maize floral phyllotaxis and early B class gene asymmetric expression are directly influenced. Finally, the functional characterization of the B class gene sts1 adds novel data regarding the formation of male and female flowers in maize. In particular, detailed analysis of sts1 expression makes clear that the establishment of floral organ identity controlled by B class genes act upstream of the carpel abortion pathway; in tassel florets, carpel abortion is controlled by the correct organ identity and not position. Raffaella Battaglia, 2015

12/2015 Weibin Song
Sosso, D et al. 2015. Nature Genetics 47:1489-1493
   Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport

Grain filling is one of the most important traits for crops to translate nutrients into seeds. Investigation on genetics factors controlling the trait will accelerate the genetic improvement in crops. In this study, Sosso and colleagues find a new and effective way to discover the evidence of genomic selection loci related to sugar transport. To identify potential targets of selection among genes that encode sugar transport proteins, they searched large-scale expression data for candidates with high expression level during seed development. Of the 54 genes analyzed, 16 were highly expressed in at least one study. Among the highly expressed genes, ZmSWEET4c was the only locus showing evidence of selection during domestication in a genomic study. As SWEETs function in sugar allocation in plants, ZmSWEET4c was made as a candidate for seed filling. Further genome-wide analysis indicated that ZmSWEET4c has lost more nucleotide diversity during domestication, particularly in the promoter and the first-intron regions. The lower nucleotide diversity in the noncoding region and the higher expression levels between 10 and 17 days after pollination (DAP) support that ZmSWEET4c was domestication related gene. Candidate gene association analysis identified significant associations between SNPs in the promoter region of ZmSWEET4c and ten-kernel and total kernel weight. These SNPs explained >4% of the total phenotypic variation for both traits and as much as 11% of their heritability. Notably, zmsweet4c insertion mutants showed dramatic loss of endosperm but slight effect on embryo development, implying ZmSWEET4c is specific to seed filling. Molecular analyses showed that ZmSWEET4c function in hexose translocation in BETL, a key tissue of endosperm responsible for the nutrients absorption. OsSWEET4, homolog of the ZmSWEET4c, in rice functions as a glucose and fructose transporter and was also a target of selection during rice domestication. These results imply that ZmSWEET4c will help us to generate new high-yield maize and rice varieties. Meanwhile, a new strategy for isolating quantitative trait loci with lower phenotypic variation and heritability was provided for researchers in this field. Weibin Song, 2015

12/2015 Michael Gore
Gerke, JP; Edwards, JW; Guill, KE; Ross-Ibarra, J; McMullen, M. 2015. Genetics. 201:1201-1211
   The genomic impacts of drift and selection for hybrid performance in maize

The work of Gerke et al. (2015) investigated the genomic impact of genetic drift and selection for maize hybrid performance in a reciprocal recurrent selection (RRS) experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations. To explore how these two evolutionary forces restructured patterns of genetic variation throughout the breeding history of both populations that were concomitantly selected for combining ability, the progenitor lines and more than 600 individuals across multiple cycles of selection (cycles 0, 4, 8, 12, and 16) were genotyped with a panel of ~40,000 genome-wide SNPs. Through a principal component analysis (PCA) of the SNP marker data set, there was found to be a gradual but continual increase in separation between the BSSS and BSCB1 populations as the experiment progressed along with clear separation of the cycles from one another within each population. This tremendous increase in genetic distance was attributed to the steady loss of genome-wide genetic diversity across cycles of selection within each population. Furthermore, a 10-fold increase in genetic differentiation, as measured by Fst, was found between the founder lines and cycle 16. As supported by computer simulations, most of the reduction in genetic diversity was the result of strong genetic drift imposed by the experimental design, even with selection for the improvement of phenotypes. In addition, the simulations showed that the level of heterozygosity within each population was lower than expected. An identify-by-descent, haplotype-based approach was used to show that the most likely targets of selection were at loci differing between the two populations, which included loci located at the low-recombination, pericentromeric regions of the maize genome. Importantly, such differential patterns of fixation provide better support for the dominance model of heterosis. Michael Gore, 2015

12/2015 Carolyn Rasmussen
Velez-Bermudez, IC et al. 2015. Plant Cell 27:3245-3259
   A MYB/ZML complex regulates wound-induced lignin genes in maize

Wounding causes lignin accumulation in plants. Lignin, formed from phenyl propanoid monomers that are assembled into higher order secondary structures, has an important function in increasing rigidity and hydrophobicity of the cell wall by binding polysaccharides. Here, the authors provide solid mechanistic evidence elucidating part of the pathway from wounding to lignin biosynthesis. First, they demonstrate that wounding or methyl-jasmonate treatment causes proteosome dependent degradation of two transcriptional repressors, MYB11 and ZML2, which in turn derepresses one of the lignin biosynthetic genes, caffeic acid O-methyl transferase (comt). MYB11 is a myeloblastosis (MYB) R2R3 type transcription factor that has an ethylene responsive element binding factor associated amphiphillic repression (EAR) domain. ZML2 is a TIFY type transcription factor whose gene expression pattern matches that of myb11. Since ZML homologs are both known to regulate wounding response and to interact with R2R3-MYB transcription factors, the authors tested their interaction. These two transcription factors physically interact with each other and their interaction requires the EAR domain of MYB11. The EAR domain is additionally required for MYB11 proteosome degradation. Both ZML2 and MYB11 bind in vivo to the comt promoter at the same time, determined by using serial chromatin immunoprecipitation (ChIP). The promoter binding sites, identified as AC-rich for MYB11 and GAT(A/C) for ZML2, in the comt promoter were 30 base pairs apart, and their model suggests that the two repressors not only bind the DNA, but also bend the DNA to bind to each other to repress comt gene expression. MYB11 and ZML2 bind promoter regions of several other lignin genes. ZML2 also interacts with two other closely related R2R3-MYB transcription factors, MYB31 and MYB42. Together, ZML2, MYB31 and MYB42 bind to the promoter of two lignin genes. The authors show that conserved cis-regulatory modules are found in several lignin genes across multiple species, suggesting a common regulatory module that controls coordinated lignin gene expression upon wounding. Carolyn G. Rasmussen, 2015

12/2015 Chung-Ju Rachel Wang
Li, Q, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1514680112
   RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

In organisms with large genomes, like maize, genes are often surrounded by hundreds of kilobases of intergenic sequence that is comprised of transposons and tandem repeats. These repetitive sequences are associated with DNA methylation, specific histone modifications that confers repressive chromatin features, called heterochromatin. However, the majority of genes (85.5%) are positioned near heterochromatic transposons (within 1 kb) in the maize genome. How chromatin structures are regulated in order to maintain the heterochromatic state for repetitive sequences and the euchromatic state for active genes is still elusive. RNA-directed DNA methylation (RdDM) is the major mechanism of de novo cytosine methylation in all CG, CHG and CHH sequence contexts (where H can be A, C or T), and it is thought to play roles in suppression of transposons and genes. The RdDM pathway is particularly important for CHH methylation, since CG and CHG methylation are primarily maintained at high fidelity following DNA replication by separate pathways. Although many components of the RdDM machinery have been identified, the downstream effects of DNA methylation remain less clear. Previous research showed that, in maize, methylated CHH (mCHH) islands are often found near genes, whereas CG and CGH methylation are associated with transposons. In this study, Li et al. analyzed whole-genome bisulfite sequencing (WGBS) data and gene expression profiles of B73 seedlings and found elevated mCHH islands distributed in the flanking regions of nearly half of the genes in maize and many conserved noncoding sequences. Their results also revealed that mCHH islands are enriched for active genes that are located close to terminal inverted repeat (TIR) DNA transposons. These mCHH islands mark a transition for CH and CHG DNA methylation that is associated with transposons. The CHH islands are relatively stable across different tissues, but show some variation among haplotypes, which are often associated with sequence insertions/deletions derived from transposon mobility. These results suggest that mCHH islands specially mark the boundaries between different types of chromatin in the maize genome. The authors further examined mCHH islands in three RdDM mutants 'mop1, mop2 and mop3' and showed that all three mutations greatly reduced mCHH levels. The loss of mCHH islands does not greatly impact gene expression, but instead leads to an additional loss of CG and CHG methylation in some transposons flanking maize genes. These results suggest that RdDM may not be a crucial requirement for the silencing of all transposons. Rather, RdDM activity and mCHH islands may be critical for creating a boundary that prevents the spread of open chromatin from active genes nearby into adjacent transposons. These results shed light on the epigenetically regulated global chromatin in plants. Rachel Wang, 2015

11/2015 Michelle Facette
Christensen, SA et al. 2015. Proc Natl Acad Sci, USA 112:11407-11412
   Maize death acids, 9-lipoxygenase-derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators

Christensen et al., isolate a new family of compounds from necrotic developing maize tissue infected with southern leaf blight. They term these new compounds 'death acids' which are specific metabolites called oxylipins that produced by lipoxygenases (LOXes). They identify a suite of death acids produced in necrotic maize tissue, and specifically characterize 10-OPEA and related compounds as locally produced phytoalexins that suppress growth of fungal pathogens and insect feeding. 13-Lipoxygenases produce the known phytohormones 12-OPDA and jasmonic acids; whereas 9-lipoxygenases produce 10-OPEA, which had a previously unknown biological function. They further show that 10-OPEA induces the expression of known defense genes in maize. They demonstrate cytotoxicity of the death acids, and go on to show the mechanism of this cytotoxicity is via cysteine proteases. The elegant and comprehensive chemistry here describe new phytoalexins that mediate local defense responses. Michelle Facette, 2015

11/2015 Michael Gore
Yang, J, et al. 2015. Plant J. 0:DOI: 10.1111/tpj.13029
   Extreme Phenotype-Genome-Wide Association Study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel

Yang et al. 2015 developed a new efficient method for complex trait dissection via a genome-wide association study (GWAS) built on the principles of bulk segregant analysis (BSA) that exploits the genotyping of phenotypically distinct pools constructed with individuals from a large diversity panel that have extreme phenotypes. This method, eXtreme Phenotype-Genome-wide Association Study (XP-GWAS), depends on the quantification of variant allele frequencies within each of the pools, followed by testing for associations between detected variants and the studied phenotypes. Not only does XP-GWAS harness the historical recombination patterns of large diversity panels to impart high mapping resolution while minimizing the number of individuals that need to be genotyped, but it also potentially enriches for rare variants that underlie extreme phenotypes and maximally exploits the most cutting-edge advances in DNA sequencing and genotyping technologies. The utility of XP-GWAS was empirically tested on the complex trait kernel row number (KRN) using a diversity panel of nearly 7,000 maize accessions from which three pools (low KRN, high KRN, and random KRN) were constructed based on reproducible phenotypic data from the Germplasm Resources Information Network (GRIN) database. The three XP-GWAS pools were genotyped using exome sequencing to estimate allele frequencies, resulting in the detection of nearly one million variants with a minimum read depth cutoff of 50X. In addition, these variants tagged nearly 90% of the high confidence maize filtered genes and were not exclusive to exonic regions of the maize genome. Through the implementation of a GWAS, 145 variants that consolidated into 121 1-kb bins distributed across the 10 chromosomes of maize were found to associate with KRN at a false discovery rate of 5%. Notably, the genomic positions for some of these associated variants significantly co-localized with regions previously detected for KRN by more conventional GWAS. Highlighting the level of resolution that it offers, with XP-GWAS it was possible to separate multiple linked QTL and resolve one of them down to a single candidate gene. The XP-GWAS approach will perhaps have its most impact in the detection of causative genes and favorable alleles in orphan crops and understudied plant species that have limited genomic resources but the availability of germplasm collections that have been phenotypically evaluated. Michael Gore, 2015

11/2015 Chung-Ju Rachel Wang
Mao, H et al. 2015. Nature Communications 6: 8326
   A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

Drought is currently one of the main constraints to crop production, which is aggravated by climate warming trends. However, identification of the genetic components underlying drought tolerance has proven to be challenging because of its complexity. In this study, Mao et al. analyzed a natural maize population, consisting of 368 inbred lines, using a genome-wide association study (GWAS) approach. By examining seedling survival rates (SR) after a severe drought treatment in six replicated experiments, phenotypic data was correlated with 560k single nucleotide polymorphisms (SNPs) in the population. The authors identified a SNP within the ZmNAC111 gene (GRMZM2G127379) that is significantly associated with plant drought tolerance (determined by the SR at seedling stage). Sequence analysis of ZmNAC111 in 262 inbred lines further showed that an 82-bp miniature inverted-repeat transposable element (MITE) is present in the ZmNAC111 promoter of drought-sensitive genotypes, such as B73 and Mo17. ZmNAC111 encodes a NAC-type transcription factor whose RNA expression is induced by drought conditions. Its induction is more significant in inbred lines without the MITE insertion (MITE-), suggesting that the MITE insertion may repress ZmNAC111 expression, resulting in higher sensitivity of MITE+ maize varieties to drought stress. Indeed, the authors found that the MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. In addition, increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes (such as NCED3, AFP3 and DREB1D) under water stress. Finally, a comparison of MITE insertion frequencies among teosinte, tropical/subtropical and temperate inbred lines suggests that the MITE insertion occurred after maize domestication from teosinte and spread in the temperate germplasm. Although it is still not clear that ZmNAC111 and its MITE allele can significantly contribute to enhancing maize yields under drought conditions in the field, this study provides a potential starting point for genetic improvements to drought tolerance in maize. Rachel Wang, 2015

11/2015 Carolyn Rasmussen
Galli, M, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1516473112
   Auxin signaling modules regulate maize inflorescence architecture

Auxin signaling is require for axillary meristem formation and therefore the development of branches and flowers. The authors demonstrate that two AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) proteins, BARREN INFLORESCENCE 1 and 4 have defects in axillary meristem formation. Normally, AUX/IAAs negatively regulate auxin signaling by sequestering AUXIN RESPONSE FACTOR (ARF) transcription factors. In the presence of auxin, the BIF proteins are degraded to release ARFs that then promote transcription. The semidominant mutants in two AUX/IAA genes, Bif1 and Bif4 have defects in axillary meristem formation. The mutations are in the conserved "degron" domain of the corresponding proteins. Mutant BIF1/BIF4 proteins are not degraded in the presence of auxin and they don't release the ARFs. The authors used an in vitro assay to demonstrate that neither mutant protein was degraded in the presence of auxin. Then, they showed that both BIF1 and BIF4 interact broadly with multiple ARFs, and that some of these ARFs in turn bind to the promoter of the transcription factor BA1. The authors propose that BIF1 and BIF4 negatively regulate the transcription of a basic helix loop helix transcription factor, BARREN STALK1 (BA1) which promotes axillary meristem formation. As auxin levels increase in the inflorescence meristem, BIF1 and BIF4 are degraded and BA1 transcription is promoted by the ARFs to produce the axillary meristem. The authors propose that after the axillary meristem is formed, auxin levels decrease inside the axillary meristem and stabilize BIF1/BIF4 to shut off BA1 transcription, thereby establishing a boundary. Carolyn G. Rasmussen, 2015

11/2015 Weibin Song
Mei, X et al. 2015. Mol Gen Genet 290:1819-1831
   Identification and characterization of paternal-preferentially expressed gene NF-YC8 in maize endosperm

NF-Y is a CCAAT-specific transcription factor that involved in the regulation of a majority of genes. Functional analysis showed that the members in this family regulate the root development, flower development, drought tolerance.The NF-Y transcription factors consist of three different subunits (A, B, and C), and more detailed information about these transcription factors in this family were summarized by Tom Laloum (Tom Laloum et al., 2013). In this study, one of the NA-YC transcription factors, named NF-YC8, was characterized genetically using the endosperm and embryo tissues generated by the reciprocal crosses between the inbred lines B73 and Mo17, Zheng58 and Chang7-2, Huang C and 178 (totally 15 NF-YC genes were identified in the maize genome). Expression analysis showed that NF-YC8 was a differential, gene-specific imprinted gene at 14 DAP and persistently imprinted throughout later endosperm development in the B73/Mo17 genetic background. Bisulfite sequencing for NF-YC8 in maize endosperm indicated that the paternal alleles were higher methylated than maternal alleles in the 5' upstream region, and the coding region was highly methylated in CG context. In addition, the protein sequences of these 15 NF-YC members were highly conserved in maize. This is the first description of maize NF-YC genes and their evolution characterization; also the first experimentally demonstrated the molecular characterization and expression pattern of NF-YC8. These results would provide more information for future investigation in maize kernel development. Weibin Song, 2015

10/2015 Chung-Ju Rachel Wang
Suzuki, M; Sato, Y; Wu, S; Kang, B-H; McCarty, DR. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00290
   Conserved functions of the MATE transporter BIG EMBRYO1 in regulation of lateral organ size and initiation rate

The shoot apical meristem produces lateral organs in a regular spacing and a regular timing, which in turn determines plant architecture. Studies in diverse plant species have suggested that the ER-localized CYP78A is required for regulating lateral organ initiation, presumably via generating a mobile signal that has not yet been identified. In this study, Suzuki et al. identified a MATE transporter, a new class of genes that is involved in in the pathway. Authors first showed the maize bige1 (big embryo1) mutant exhibited accelerated leaf and root initiation as well as enlargement of the embryo scutellum, that are similar to phenotypes observed in cyp78a mutants in diverse plant species. Studies revealed that Bige1 gene encodes a MATE transporter protein, localized to the proximal, trans-Golgi, indicating a possible role in secretion of a signaling molecule. Interestingly, CYP78A/ZmGe1 gene is upregulated in bige1 mutant embryo, suggesting a role for BIGE1 in feedback regulation of a CYP89A pathway. Authors further showed that Arabidopsis bige1a, bige1b single mutant and bige1a bige1b double mutant exhibited increased rosette leaf number, and their phenotype can be complemented by maize Bige1, showing that the BIGE1 transporter has a conserved function in regulation of lateral organ in plants. Although the mobile signals are still unknown, it is plausible that CYP78A and BIGE1 play roles in biosynthesis and movement of small molecules, respectively. Rachel Chung-Ju Wang, 2015

10/2015 Weibin Song
Grimault, A, et al. 2015. Plant J. 0:doi: 10.1111/tpj.13024
   ZmZHOUPI, an endosperm-specific bHLH transcription factor involved in maize seed development

The embryo and the endosperm could be used as the ideal targets for the study of gene interaction. In this study, the authors identified one bHLH transcription factor named ZmZOU. This gene was the homolog of AtZOU in Arabidopsis. Expressing analysis showed that ZmZOU was the endosperm specific. During maize kernel development, ZmZOU exhibited a high expression level between 9 and 35 days after pollination (DAP) with a peak at 20 DAP. This corresponds to the end of the early development phase (1 to 12DAP) and the entire filling stage (12 to 35 DAP). Within the kernel, ZmZOU expression was limited to the endosperm. Although no precise spatial expression pattern could be established within the endosperm, additional qRT-PCR experiments on the top and bottom and adaxial and abaxial parts of the kernel clearly demonstrated that the expression domain of ZmZOU is much more extensive than that of the ZmEsr2 and ZmLec1 marker genes for the ESR and the embryo, respectively. Transgenic ZmZOU-RNA interference (RNAi) lines were generated with RNAi constructs under the control of the constitutive rice Actin promoter. Phenotyping of the transgenic lines showed that the t ZmZOU knock down did not significantly modify endosperm growth but slightly impeded embryo growth at early stages. The stomatal development in the leaf was affected in the transgenic line of ectopic expression of ZmZOU. Further protein interaction study revealed that the ZmZOU interacts with ZmICE proteins that were also predicted to encode a bHLH transcription factor, which indicated that ZmZOU form a complex with other members of bHLH class during the activation of downstream genes or DNA binding progress. The results here provided us more information about the function of this family member in maize and the functional diversity between different species. The identification and characterization of the regulated genes by ZmZOU will provide us more information about the genetic basements for the interaction between the embryo and endosperm. Weibin Song, 2015

10/2015 Michael Gore
Bian, Y; Holland, JB. 2015. G3 5:2073-2084
   Ensemble learning of QTL models improves prediction of complex traits

QTL data can be found here.

The genetic dissection of complex traits by QTL linkage analysis in experimental populations offers higher mapping resolution (i.e., smaller marker intervals) when harnessing highly saturated linkage maps. However, increased marker densities may also have negative consequences as multicollinearity among tightly linked genetic markers could confound the detection of QTL and estimation of their effects as well as increase the chance of overfitted QTL models with poor predictive performance. Considering this need, Bian and Holland (2015) developed a new ensemble (machine) learning approach¿¿¿the thinning and aggregating (TAGGING) method¿¿¿where a collection of QTL mapping models are individually trained in parallel on a set of disjoint linkage maps of thinned marker density resulting from a stratified sampling approach, followed by the aggregation of their prediction results with a model averaging procedure. The two authors tested the TAGGING method using cross validation of empirical complex trait data (southern leaf blight, plant height, and days to anthesis) from the maize nested association mapping (NAM) panel in the context of two QTL mapping models: (1) joint-family (JF) linkage analysis for multi-family mapping populations, and (2) single-family (SF) QTL analysis for biparental mapping populations. It was found that among the four tested models, the ensemble joint family linkage (EJF), ensemble single family (ESF), JF, and SF, the EJF models provided the highest prediction ability across all traits, thinning intensities, and QTL selection stringency thresholds. Such a result implies that the TAGGING method assisted the JF analysis to better model the genetic architecture of these three complex traits. In addition, TAGGING of JF and SF models consistently reduced both the variance and bias in prediction for all traits and under all selection thresholds. Interestingly, an ensemble model that united predictions from TAGGING-assisted QTL and infinitesimal (GBLUP) models enhanced prediction abilities, suggesting that the ensembling of both models parlayed complementarities for a truer depiction of the genetic architectures. Taken together, TAGGING has the high potential to provide insights into the genetic architecture of complex traits (QTL position and corresponding effect sizes along with their precision) while improving prediction ability in genetic studies and breeding programs, all of which anchored to highly dense linkage maps. Michael Gore 2015

10/2015 Raffaella Battaglia
Lee, DH, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00434
   The axial element protein DESYNAPTIC2 mediates meiotic double-strand break formation and synaptonemal complex assembly in maize

The Authors studied the functional roles of the maize DESYNAPTIC2 (DSY2) protein during meiosis, the specified cell division to produce haploid cells during sexual reproduction, and revealed the novel insights in homologous chromosome pairing and meiotic synapsis in plants. The original dsy2 mutant was isolated 30 years ago with sterile phenotype. They first identified the gene by map-based cloning using the Sequenom SNP assay in a F2 population that contained segregated dsy2 mutant and phenotypic wild-type plants. To better understand its role, they utilized super-resolution microscope to examine its subcellular localization and showed that DSY2 protein is located on meiotic chromosome axes as a component of the synaptonemal complex, an important protein complex in meiosis. Examination of serial events during meiotic recombination demonstrated that DSY2 is involved in the DNA double strand break formation, the essential step of homologous chromosome pairing. More importantly, studies showed that loss of DSY2 disrupted the synaptonemal complex assembly as the central element fails to load between the chromosome axes in the dsy2 cells. By yeast-two-hybrid and Bimolecular Fluorescence Complementation experiments, the Authors revealed that DSY2 interacts with the central element protein ZYP1, and this finding accounts for the synaptic phenotype observed in the dsy2 mutant. Therefore, DSY2, a chromosome axis protein, not only mediates DNA double strand break formation, but also bridges the chromosome axis and central element during synapsis. This work presented evidence for the first time of the mechanism for the synaptonemal complex assembly at the molecular level. Raffaella Battaglia, 2015

10/2015 Carolyn Rasmussen
Baute, J, et al. 2015. Genome Biol. 16:168
   Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

The authors use a recombinant inbred line (RIL) population originating from a cross between B73 and H99 inbred lines to correlate transcript abundance with leaf traits. RNA-sequencing was performed on the most basal 0.5 cm of the division zone (the base of the leaf where division occurs) from leaf four of 103 different RILs and transcript abundance was compared with measurements of leaf and shoot traits. The traits measured were final leaf size traits (length, area, width and weight), shoot traits (dry and wet weight of the entire above-ground tissue) as well as dynamic growth conditions of the leaf such as leaf elongation rate, leaf elongation duration, the timing of leaf emergence and other events. Intriguingly, a positive correlation between the size of the division zone and final leaf size traits was observed, suggesting that differentially expressed genes within the division zone may be relevant targets for crop improvement. Analysis was focused on the top 1% of correlating or anti-correlating ((anti-)correlating) genes between traits. Of the 1740 genes with expression patterns that (anti-)correlated with at least one trait, ~50% were specific for just one trait. Interestingly, genes with expression levels that (anti-)correlated with final leaf size traits, dynamic leaf traits and shoot weights were then placed into functional categories and compared with Arabidopsis thaliana orthologs and their corresponding mutant phenotypes. Although highly divergent genes (those with more than 1.75% single nucleotide polymorphisms) were eliminated from analysis, it is an important step forward in identifying correlations between gene expression levels and leaf and shoot traits for both known and uncharacterized novel genes. Carolyn Rasmussen, 2015

9/2015 Michelle Facette
Kir, G, et al. 2015. Plant Physiol. 0:DOI: 10.1104/pp.15.00367
   RNAi knockdown of BRI1 in maize (Zea mays) reveals novel functions for brassinosteroid signaling in controlling plant architecture

In this paper, the authors characterize the role of brassinosteroids (BRs) in maize growth by knocking down orthologs of the leucine rich repeat receptor like kinase, BRI1, which has been previously demonstrated in arabidopsis to be the BR receptor. RNAi lines that knock down the maize Bri1 and Bri1-like (BRL) genes plants show defects in growth (such as internode elongation) and BR response, similar to the arabidopsis and rice bri1 mutants. Moreover, kinematic analyses demonstrate that the growth defects are due to both a reduction in cell elongation and cell division. They created a YFP reporter line of the maize ortholog of the BR-responsive transcription factor, BES1. As expected, BES1-YFP was responsive to BR, and interestingly, was enriched in a developing leaves in a band which will eventually determine the auricle and ligule. The RNAi lines also showed a defect in auricle development, resulting in an increase in leaf angle. The RNAi lines shared phenotypes with the maize mutant Rough Sheath-O (Rs-O) and thus determined if BR gene expression was altered in Rs mutants, or vice versa. Expression of marker genes suggested that while there appears to be small changes in BR genes in Rs-O mutants, there was no indication of BR regulating Rs.Together these data work towards a more comprehensive understanding of BR regulation in maize, and how it might contribute to agronomically important traits such as dwarfism and leaf angle. Michelle Facette, 2015

9/2015 Michael Gore
Technow, F; Messina, C; Totir, LR; Cooper, M. 2015. PLoS One. 10:e0130855
   Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

When built on accurate whole-genome prediction (WGP) methods, genomic selection (GS) can accelerate the breeding cycle of crops by enhancing genetic gain per unit time. Efforts to improve the accuracies of whole-genome enabled predictions have relied on the development and refinement of linear regression models (e.g., the Bayesian alphabet), maximization of genome-wide marker density, and optimization of training population designs. In contrast to additive effects, the prediction of nonlinear, epistatic effects for complex traits, however, remains a challenge for WGP models. This is especially of concern given that grain yield and other important physiological traits can be the product of both additive and non-additive (multiplicative) effects. Additionally, the ability to predict genotype-by-environment (GxE) interactions for specific environments with WGP models is still in its infancy. To model both non-linear effects and GxE interactions, Technow et al. (2015) incorporated a dynamic crop growth model (CGM), which explicitly incorporates biological and environmental information relating to the physiological mechanisms responsible for crop performance, in WGP of yield as a complex trait in maize. This novel incorporation of a CGM was enabled through the use of an approximate Bayesian computation (ABC) method that replaces a likelihood function with a more tractable simulation step. The performance of the CGM-WGP method for grain yield was superior in terms of prediction accuracy to a standard WGP method without CGM (GBLUP) on a synthetic data set (i.e., simulated genotype and phenotype data for a biparental double-haploid population and observed environmental data across two years) because it better modeled non-additive effects. Notably, the non-additive effects on grain yield were the product of non-linear functional relationships between grain yield and physiological traits. This was especially strong between grain yield and total leaf number, a relationship following an optimum curve. Interestingly, the CGM-WGP method also succeeded at better predicting performance than GBLUP in unobserved environments, as an example, the use of models fitted with 2012 data to predict performance in 2013. Such a result suggested that the CGM-WGP method was more successful at predicting GxE interactions. The findings of this study show that the use of CGM-WGP in the estimation of marker effects across the genome offers higher prediction accuracies than WGP alone, providing a novel method with tremendous potential that can even be further improved with more advanced CGMs and ABC algorithms. The next most important step, however, is to empirically test CGM-WGP in breeding programs of maize and other crops. Michael Gore, 2015

9/2015 Weibin Song
Feng, Y, et al. 2015. Theor Appl Genet. 0:DOI: 10.1007/s00122-015-2589-7
   Multiple loci not only Rf3 involved in the restoration ability of pollen fertility, anther exsertion and pollen shedding to S type cytoplasmic male sterile in maize

Cytoplasmic male sterility (CMS) has been used for hybrid seed production in maize. However, the molecular mechanisms for CMS, specifically for the S type, are not clear enough. Fertility restoration to CMS-S was considered mainly controlled by a single locus named Rf3, which has been mapped to the long arm of chromosome 2 more than 30 years ago, but not cloned yet. In this study, Feng and colleagues focused on the genome wide analysis of the genetic loci associated with the restoration ability to CMS-S. Three fertility related traits (including pollen fertility, anther exsertion and pollen shedding) were used to GWAS study. Firstly, the correlation analysis among the traits showed that Positive, strong correlations were displayed for pollen fertility investigated under the three environments, and correlations of anther exsertion and pollen shedding under different environments were also significant. The three traits were highly correlated with each other. Then, the genome-wide association mapping for the three traits was investigated, which showed that 19, 3 and 8 significant loci for pollen fertility, anther exsertion and pollen shedding were identified, respectively. Individual locus explained up to 28.26 % of phenotypic variation. Of them, only Rf3, the main restorer-fertility gene of CMS-S, was identified for the three traits simultaneously. The results here further verified the complexity of the genetic architecture of fertility restoration to CMS-S, and will accelerate the cloning of the classical restoration gene for CMS-S in maize. Weibin Song, 2015

9/2015 Carolyn Rasmussen
Yu, P; Eggert, K; Von Wiren, N; Li, CJ; Hochholdinger, F. 2015. Plant Physiol. 0:DOI: 10.1104/pp.15.00888
   Cell-type specific gene expression analyses by RNA-Seq reveal local high nitrate triggered lateral root initiation in shoot-borne roots of maize by modulating auxin-related cell cycle-regulation

Yu et al demonstrated that locally applied nitrate induced lateral root development by increasing cell division in phloem-pole pericycle cells. Local auxin transport and accumulation of auxin in the stele was observed before lateral root emergence. RNA-sequencing of the stele was used to determine changes in expression patterns between low nitrate and high nitrate conditions. They identified increased expression of positive regulators of the cell cycle (cyclin dependent kinases) and reduced expression of negative regulators of the cell cycle (KRPs) as well as increased expression of several auxin transporters (PIN1a, PIN1c and PIN9) and the ubiquitin dependent protein degradation machinery under high nitrate conditions. Laser capture microdissection was used to show that PIN9 expression increased in endodermis, pericycle and phloem after nitrate treatment while PIN1a expression was increased in the pericycle and the phloem. Their model suggests that high nitrate promotes basipetal auxin transport mediated by PIN1a and PIN1c, while PIN9 transports auxin into pericycle cells. Then auxin directly or indirectly via ubiquitin dependent protein degradation machinery promoted degradation of proteins that block cell cycle progression as well as increased expression of positive regulators of the cell cycle in the stele. This elegant study showed that adult maize roots develop lateral roots in response to nitrate via auxin mediated resumption of cell cycle progression in pericycle cells. Carolyn G. Rasmussen, 2015

9/2015 Chung-Ju Rachel Wang
Svitashev, SK et al. 2015. Plant Physiol 169:931-945
   Targeted mutagenesis, precise gene editing and site-specific gene insertion in maize using Cas9 and guide RNA

Targeted genome editing technologies such as CRISPR/Cas9 utilize engineered nuclease to create targeted DNA double-stand breaks (DSBs), and DSBs can then be repaired by either non-homologous end-joining (NHEJ) or homology-directed repairing (HDR) pathway, depending whether a homologous template is available in the same cell. The NHEJ is prone to imperfect repair, which results in mutations with small deletion or insertions. HDR, on the other hand, can be exploited to achieve precise gene modification by homologous recombination with the desired repair template. The CRISPR/Cas9 system has been shown to function in many plants, including maize. However, these studies reported mutations via NHEJ, rather than precise gene editing. In this paper, Svitashev et al. expressed maize codon-optimized Cas9 endonuclease and single guide RNAs (gRNA) with or without DNA repair template, by biolistic transformation, targeting five different genes in immature maize embryos. Frist of all, by sequencing amplicon at the target sites, the simple Cas9-gRNA experiment without DNA repair template yielded mutation frequencies greater than 1.3 %. It can also simultaneously introduce mutations at multiple loci in a single transformation experiment. They also demonstrated that delivery of gRNA in the form of RNA molecules or DNA vectors into maize cells containing a pre-integrated Cas9 is feasible for the generation of mutations. Then, they tested precise gene editing by co-transforming either single-stranded oligonucleotides or double-stranded DNA vectors as repair templates, and both experiments produced precise single nucleotide change in the ALS2 gene which confers maize plants resistant to chlorsulfuron, an herbicide. Progeny exhibited expected Mendelian segregation of mutations, edits, and targeted gene insertions. This proof-of-principle study nicely demonstrated the utility of Cas9-gRNA technology as a maize genome editing tool. Rachel Chung-Ju Wang, 2015

8/2015 Weibin Song
Grimault, A et al. 2015. Plant Sci 236:116-125
   Role of B3 domain transcription factors of the AFL family in maize kernel filling

The trait of kernel filling is important for yield, and many QTLs have been identified using different linkage population. But no QTLs controlling the kernel filling were cloned so far. In this paper, Grimault et al. characterized the functional roles of the AFL gene family members (belonging to B3 domain transcription factor) during the kernel filling stage. Among the five ZmAFL genes identified in the maize genome, ZmAFL4, like LEC2, has preferential gene activity in pollen and seed, although its seed gene activity is restricted to the endosperm during reserve accumulation. Knock down of ZmAFL4 gene activity perturbs carbon metabolism and reduces starch content in the developing endosperm at 20 DAP. ZmAFL4 and ZmAFL3/ZmVp1 trans-activate a maize oleosin promoter in a heterologous moss system. These results suggest that the functions of some members of this family could be conserved between dicot and monocot species, and provided us many new candidates for further research the complex trait: kernel filling. Weibin Song, 2015

8/2015 Chung-Ju Rachel Wang
Wang, H; Studer, AJ; Zhao, Q; Meeley, RB; Doebley, JF. 2015. Genetics. 200:965-974
   Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in tga1

Maize is remarkably dissimilar to its wild ancestor teosinte, which makes it an extremely interesting model for the study of domestication. A single gene, teosinte glume architecture1 (tga1), encoding a SBP-box transcriptional regulator, has been identified as the gene conferring encased teosinte kernels into naked maize kernels. In this study, Wang et al showed that a single fixed nucleotide difference between maize and teosinte in the tga1 coding sequence, leading to an amino acid substitution (Lys in teosinte to Asn in maize at the sixth amino acid position), is the causal variant that underlies the origin of the naked maize grains. The protoplast transient assays with effector and reporter constructs showed that Lys-Asn substitution makes the maize-TGA1 a strong transcriptional suppressor. Although maize -TGA1 and teosinte-TGA1 show no difference on binding site specificity for the GTAC motif, maize-TGA1 was found to form more stable dimers than teosinte-TGA1. Authors also explained their previous observation that higher TGA1 protein abundance detected in teosinte is likely due to a tightly linked paralog of tga1, called not1, whose protein product can be also recognized by the anti-TGA1 antibody. Together with the fact that the not1 null allele has no phenotype, these results support the model that the single amino acid substitution in TGA1 controls this kernel trait between maize and teosinte. Authors also described the pleiotropic effects of RNAi lines for tga1, indicating that tga1 may play a broad role in development. Interestingly, tga1-RNAi maize plants display some characteristics of the tga1-teosinte glume phenotype, suggesting that Lys-Asn from teosinte to maize is a gain-of-function mutation. This paper showed a nice example how a simple amino acid change can alter protein function and thereby drive morphological evolution. Rachel Wang, 2015

8/2015 Carolyn Rasmussen
Nuccio, ML, et al. 2015. Nature Biotechnology. 33:862-869
   Expression of trehalose-6-phosphate phosphatase in maize ears improves yield in well-watered and drought conditions

Several independent multi-year and multi-location field studies were used to demonstrate that maize lines expressing trehalose-6-phosphate phosphatase (TPP) specifically in young ear tissues produced an average of 0.5 metric ton per hectare more than non-transgenic controls under drought conditions. Large increases in yield were observed in well-watered or mild-drought conditions (9%-49%) and severe drought conditions (31%-123%). The increased yield was due to increased sucrose allocation to ear spikelets leading to increased kernel set. TPP converts trehalose-6-phosphate (T6P) to trehalose. T6P, a molecule known to coordinate sucrose levels with plant development via negative regulation of the protein kinase SnRK1, was reduced in plants expressing TPP while sucrose was increased. To reduce pleotropic effects that would be caused by global TPP expression, a rice transcriptional regulator Mads6 promoter was used to express TPP in the following parts of the ear: the node, vasculature and spikelet. Use of another promoter with similar but lower expression in the ear node and vasculature had a detrimental effect on yield. Importantly, rigorous field tests were done over multiple years, locations and germplasm adapted to the field locations to show that OsMads6-TPP1 significantly and consistently increased yield, particularly in drought conditions. Carolyn G. Rasmussen, 2015

Transgenic OsMads6-TPP1, over expressed in ears, results in higher yields, especially under drought conditions.

8/2015 Raffaella Battaglia
Shi, JR et al. 2015. Plant Physiol pp.doi: 10.1104/pp.15.00780
   Over-expression of ARGOS genes modifies plant sensitivity to ethylene, leading to improved drought tolerance in both Arabidopsis and maize

The Authors investigate the functional role of the maize and Arabidopsis ARGOS genes. As a first approach they over-express the Zm-ARGOS1 gene in Arabidopsis obtaining transgenic plants with a phenotype similar to the ethylene insensitive mutants ethylene response 1 (etr1-1) and ethylene-insensitive 2 (ein2-1). To better understand whether the Zm-ARGOS1 gene might be involved in the ethylene pathway, the Authors analyze the phenotype of 35S:Zm-ARGOS1 seedlings germinated in presence of ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Interestingly, the 35S:Zm-ARGOS1 plants are insensitive to exogenous ethylene. The ethylene insensitiveness is further confirmed with different approaches and also testing the Zm-ARGOS8, At-ARGOS-LIKE2 (At-ARL2) and At-ARL3 genes. Next, Shi and colleagues aim to understand whether the Zm-ARGOS1 gene acts in the ethylene pathway. They therefore introduce the 35S:Zm-ARGOS1 construct into the ctr1-1 mutant background where the ethylene signal is suppressed. The results that they obtain indicate that the signaling pathway downstream of CTR1 functions properly even in the presence of over-expressed Zm-ARGOS1. In wild-type plants, the activity of the ethylene receptor in modified by the interaction of the REVERSION-TO-ETHYLENE-SENSITIVITY1 (RTE1) and ETR1 factors. The observation that the ethylene insensitive phenotype decreases when the Zm-ARGOS1 gene is over expressed in the etr1-7 rte1-2 double mutant background makes the Authors suggest that Zm-ARGOS1 may act between the ethylene receptor and CTR1, affecting ethylene perception or the early stages of ethylene signal transduction. Arabidopsis plants over expressing the Zm-ARGOs genes show increased drought tolerance and, interestingly, the over expression of the Zm-ARGOS8 gene in maize leads to increased grain yield under field conditions. Raffaella Battaglia 2015

8/2015 Michael Gore
Lipka, AE, et al. 2013. G3. 3:1287-1299
   Genome-wide association study and pathway-level analysis of tocochromanol levels in maize grain

Table S7 of the paper lists SNPs associated with 4 tocopherol/tocotrienols grain traits.

Tocochromanols, a group of structurally related compounds that include tocopherols and tocotrienols, are the predominant lipid-soluble antioxidants in maize grain. For each of these two compound classes, there are four species (alpha, beta, delta, and gamma) of compounds distinguished by the degree and position of methyl groups on an aromatic ring. Of these eight compounds, alpha-tocopherol has the greatest vitamin E activity, but tocotrienols appear to have greater antioxidant capacity. Although overt vitamin E deficiency is rare, an estimated more than 90% of Americans have a diet that is insufficient in vitamin E. Notably, suboptimal dietary intake of vitamin E has been linked to increases in risk to cardiovascular disease and some cancers. Maize grain and its derivative oil products primarily consist of the lower vitamin E activity gamma tocopherol, thus genomics-assisted breeding efforts are needed to increase levels of alpha-tocopherol. Through a genome-wide association study and pathway level analysis of a 281-member maize inbred panel scored with more than a half million SNP markers, Lipka et al. 2013 identified key loci controlling levels of tocochromanols in maize grain. Even though the panel did not provide sufficient statistical power at the genome-wide level to detect rare causative alleles from tropical germplasm, a new association between ZmVTE1 (tocopherol cyclase) and tocotrienol composition was detected along with the identification of a ZmVTE4 (gamma-tocopherol methyltransferase) haplotype that had a nearly six-fold difference in alpha-tocopherol levels between least and most favorable haplotype classes. In the pathway-level analysis, ZmHGGT1 (homogentisate geranylgeranyltransferase) and a prephenate dehydratase parolog (one of four in the maize genome) were found to modestly regulate tocotrienol levels. The allelic variation at these four loci have the potential to be harnessed in maize biofortification breeding programs for optimizing the profile of vitamin E and antioxidant levels in grain. Michael Gore, 2015

8/2015 Michelle Facette
Hurni, S, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1502522112
   The maize disease resistance gene Htn1 against northern corn leaf blight encodes a wall-associated receptor-like kinase

The authors identify the gene Htn1, which confers resistance to the maize pathogen that causes Northern Leaf Blight (NLB). A dominant allele of Htn1 was identified from a Mexican land race of maize, and together with other Htn loci this gene confers resistance to many commercial lines. Map-based cloning of the Htn1 gene identified a region containing two wall-associated kinases (WAKs), and a third, related protein that has the extracellular domain of WAKs but not the intracellular kinase domain. Using the parental mapping lines that contain the resistant Htn1 allele, the authors isolated multiple TILLING mutants in each of the two WAKs, and analyzed these lines for NLB resistance. From this analysis they concluded one of the WAKs (ZmWAK-RLK1) was responsible for NLB resistance. Comparison of the protein sequence in the resistant line to a susceptible line showed that while the intracellular kinase domains are very similar, the extracellular (receptor) domain was diverged. The discovery of a WAK as a resistance protein suggests that it may either act as a receptor that detects fungal- or plant-derived molecules that act as elicitors. Alternatively, since WAKs bind to cell walls, which is a novel property amongst plant receptors, this WAK may directly detect cell wall alterations caused by fungal penetration. Further analysis of this important gene allele will surely forward our understanding of plant-pathogen interactions and the relationship between cell walls and plant defense. Michelle Facette, 2015

7/2015 Carolyn Rasmussen
Zhan, A et al. 2015. Plant Physiol pp.DOI:10.1104/pp.15.00187
   Reduced lateral root branching density improves drought tolerance in maize

The authors compared maize recombinant inbred lines (RILs) that had many short lateral roots to those RILs that had few but long lateral roots under water stress conditions. RILs with few but long lateral roots had a greater ability than RILs with many short lateral roots to acquire water under water stress conditions. The ability to acquire water provided the plants with few long lateral roots with better drought tolerance, which was assessed by comparing leaf relative water content, yield, carbon dioxide exchange, and root respiration under well watered and water stress conditions. They also measured the isotopic ratios of water to see where in the soil the plant's water was acquired. The few but long lateral roots were able to gather water from deeper within the soil, which allowed increased plant growth and yield. Importantly, the authors used three distinct environments to perform water stress experiments: a greenhouse mesocosm, and two spatially separated fields. The results showed the same trends in all three environments suggesting that few and long lateral roots may provide better water acquisition across different soil types and other environmental factors. In almost every case the phenotype of the roots were consistent across different environmental conditions indicating genetic control of this phenotype. Together, these data suggest that the few but long lateral root phenotype may be helpful for improving drought tolerance in maize. Carolyn Rasmussen, 2015

7/2015 Michelle Facette
Redkar, A et al. 2015. Plant Cell 27:1332-1351
   A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors

Ustilago maydis is a biotrophic fungus that infects many different maize tissues. Like all pathogens, U. maydis secretes effector molecules that help promote the infection and colonization process. In turn, these effectors are sometimes recognized by the plant, and promote defense responses. This paper characterizes the U. maydis secreted effector protein See1, and it's interactions in maize. The authors determine the See1 effector is required for induction of leaf tumors in maize; but not tassel or ear tumors. Transcriptomic analyses and analysis of DNA synthesis in infected tissues indicate a role for See1 in promoting DNA replication in infected tissues. A yeast 2-hybrid screen revealed that See1 interacts with the maize ortholog of SGT1, a regulator of cell cycle progression previously shown to be involved in defense responses in plants. The authors confirm this interaction using immunoprecipitation and BiFC, and show that See1 and SGT1 localize to the cytoplasm and nucleus in plant cells. They further show that See1 interferes with the phosphorylation of SGT1 in planta, thus suggesting a molecular mechanism for infection. Specifically, they suggest that the suppression of SGT1 phosphorylation by See1 results in suppression of defense responses and/or promotion of the cell cycle. Michelle Facette, 2015

Other maize Genes possibly involved in the interaction reported in this paper are: maize MAPK kinase 2, NP_001104843.1; maize putative MAPK family protein, AFW85791.1; maize putative MAPK MPK6, ACG37232.1; maize ABA stimulation MAPK, NP_001152745.1; maize unknown kinase, ACF85409.1. maize MAPK kinase 2, NP_001104843.1; BLASTs to GRMZM2G020216 (98% ident). Second hit GRMZM2G002100 (92% ident.) maize putative MAPK family protein, AFW85791.1; BLASTs to GRMZM2G020216 (100% ident). Second hit GRMZM2G002100 (94% ident.) maize putative MAPK MPK6, ACG37232.1; BLASTs to GRMZM2G020216 (99% ident). Second hit GRMZM2G002100 (93% ident.) maize ABA stimulation MAPK, NP_001152745.1; BLASTs to GRMZM2G002100 (98% ident). Second hit GRMZM2G020216 (93% ident.) maize unknown kinase, ACF85409.1. BLASTs to GRMZM2G002100 (100% ident). Second hit GRMZM2G020216 (94% ident.)

7/2015 Michael Gore
Chandler, KL, et al. 2013. Crop Sci. 53:189-213
   Genetic Analysis of Visually Scored Orange Kernel Color in Maize

Maize is an important staple crop in many of the countries where vitamin A deficiency is present and has considerable genetic variation for carotenoid grain levels. However, the varieties of maize grain typically used for human consumption do not provide adequate daily levels of provitamin A carotenoids. White grain maize has minimal levels of carotenoids and it is highly preferred over yellow maize for human consumption in East and southern Africa. Yellow grain maize has appreciable levels of carotenoids, but is viewed as inferior in these countries due in part to its negative association with imported relief food, animal feed, and unfavorable taste and texture. However, recent studies are showing that there does not appear to be strong aversion to orange maize that has higher levels of provitamin A carotenoids. Chandler et al. (2013) showed that orange kernel color has a heritable basis, and a significant proportion of the phenotypic variation in this color trait appears to be regulated by QTL proximal to carotenoid biosynthesis and degradation genes. Results from this study provide evidence that orange kernel color should respond favorably to visual selection for increasing total carotenoids and can be further enhanced by marker-assisted selection of carotenoid synthesis and degradation genes directly influencing composition to increase provitamin A levels in maize grain. Michael Allen Gore, 2015

7/2015 Raffaella Battaglia
Nelissen, H et al. 2015. Plant Cell pp.doi: 10.1105/tpc.15.00269
   Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf

The Authors study the changes in composition of the AN3-associated SWI/SNF complex in diving and expanding cellular domains of the maize leaf. The Tandem Affinity Purification (TAP) approach is used to purify the proteins associated to the ANGUSTIFOLIA3 (AN3/GIF1) factor in different areas of the growing maize leaf; the purified proteins are then analyzed on a mass spectrometer. Interestingly, the Authors identify a core complex that is highly conserved between eukaryotes; this complex is then recruited to the target DNA by growth process-specific GROWTH REGULATING FACTORS (GRFs). While the GRF1 factor is highly represented as associated AN3 protein in dividing tissues, the GRF4 and GRF10 factors are more abundant in expanding tissues. The model proposed by the Authors show that, in the maize leaf, the balance between different GRFs associated to the AN3/GIF1 factor determines the transition between diving and expanding tissues. Together with elucidating the molecular processes occurring in the growing maize leaf, the paper from Nelissen et al. puts the basis to improve the study of protein complexes with a dynamic perspective. Raffaella Battagila, 2015

7/2015 Chung-Ju Rachel Wang
Mascheretti, I et al. 2015. Plant Physiol 168:1351-1363
   Florigen-encoding genes of day-neutral and photoperiod-sensitive maize are regulated by different chromatin modifications at the floral transition

It has been known that floral regulatory pathway, including autonomous, and photoperiod controls the expression of florigen genes, and in turn promotes the transition from vegetative to reproductive development via long-distance trafficking from leaf to the shoot apical meristem. Maize is considered to be either a day-neutral plant (such as the temperate maize line B73) or a short-day plant (such as tropical maize lines). Teosinte, the maize progenitor found in tropical environments, is also sensitive to day lengths and its transition from vegetative to reproductive development can be induced by short-day treatment. In maize, the ZCN8 gene was shown to have florigenic activity. The indeterminate1 (id1) gene, encoding a zinc finger protein, is known to promote the ZCN8 expression in mature leaf of B73. However, ZCN8 gene is unlikely a direct target of ID1, because they are expressed during different stages of leaf development. On the other hand, in tropical maize, the short-day photoperiod is able to induce ZCN8 gene expression. These different floral induction controls in maize provide a unique opportunity to study mechanisms regulating ZCN gene expression between the autonomous and photoperiod pathways. In this study, the expression and associated-epigenetic markers of two maize florigen genes (ZCN7 and ZCN8) were studied in B73 (normal flowering), the id1 mutant (unable to flower), and tropical teosinte under floral-inductive and non-inductive photoperiods. Mascheretti et al revealed that histone H3 acetylation in ZCN7/ZCN8 chromatin are associated with competence to flower in response to id1 gene activity in temperate B73. However, in teosinte, different histone markers (H3K4me2, and H3K4me3) are associated with floral-inductive teosinte samples. Finally, authors proposed a model that in temperate maize, id1 is expressed in developing leaves to establish a transcriptionally competent chromatin state that later allows expression of ZCN7/ZCN8 in mature leaf. In tropical maize, floral induction is dependent on short-day photoperiods and the circadian clock to activate florigen expression via epigenetic control on different histone modifications. Chung-Ju Rachel Wang, 2015

7/2015 Weibin Song
La Rocca, N, et al. 2015. J Exp Bot. 0:doi:10.1093/jxb/erv278
   The maize fused leaves1 (fdl1) gene controls organ separation in the embryo and seedling shoot and promotes coleoptile opening

Seedling architecture is more related to the embryo development, and some genetic mutation during the embryogenesis will affect the seedling architecture, as cr4 and dek1 mutant affected both the seedling leaf and kernel in maize. In this study, Nicoletta and colleagues have cloned and characterized the mutant fdl1-1 that was isolated by an Enhancer/Suppressor mutator (En/Spm) element insertion located in the third exon of the gene, identifies a novel gene encoding ZmMYB94, a transcription factor of the R2R3-MYB subfamily. This gene has been cloned through co-segregation analysis, and verified by the RNAi method. Further analysis showed that Fdl1 is involved in the regulation of cuticle deposition in young seedlings as well as in the establishment of a regular pattern of epicuticular wax deposition on the epidermis of young leaves. loss of Fdl1 action also correlates with developmental defects, such as delayed germination and seedling growth, abnormal coleoptile opening and so on. qPCR indicated that high expression was observed in the embryo, in the seedling coleoptile and in the first two leaves, whereas RNA level, as well as phenotypic defects, decreases at the third leaf stage. Interestingly several of the Arabidopsis MYB genes most closely related to ZmMYB94 are also involved in the activation of cuticular wax biosynthesis, suggesting deep conservation of regulatory processes related to cuticular wax deposition between monocots and dicots. Since several MYB genes in maize are involved in the control of the phenylpropanoid metabolic pathway, Fdl1 has provided a new role of ZmMYB family members during the maize embryo development for us. Weibin Song, 2015

6/2015 Chung-Ju Rachel Wang
Yu, CP, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1500605112
   Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

The gene regulatory network that controls maize leaf development is still not well understood. This knowledge may be useful for developing C3 crops to perform C4 photosynthesis for enhanced yields in a long run. In this study, Yu et al studied 22 transcriptomes of developing maize leave from dry seeds to 192 hours post imbibition. Through coexpression and differential gene expression analysis, authors identified functional transitions with molecular signatures during leaf development. Interestingly, authors analyzed expressions of transcription factors (TFs) among 22 samples, and highlighted the key TF families involved in developmental and physiological processes. More significantly, authors used maize genomic sequences and transcriptomic data or used the known TFs and its transcription factor binding sites (TFBS) in rice and Arabidopsis to predict maize TF-TFBS pairs during leaf development. In total, about 1300 novel TFBSs and 253 new TF-TFBS pairs were identified in maize. This dataset will serve as the foundation for a systems biology approach to the understanding of regulatory network involved in maize leaf development. Rachel Wang, 2015

Chun-Ping and colleagues use an extensive data set to finely describe the transcriptional changes that occur during leaf development in maize. The authors analyze 22 transcriptomes with a time span from hour 0 (dry seeds, T000) to 192 h post imbibition (T192). The possibility of having this large dataset allows to precisely identify genes that are coregulated and involved in the same biological processes. 30 co-expressed modules are divide into three stages and different criteria are used to define Differentially Expressed Genes (DEGs). Focusing on Transcription Factors (TFs), the authors describe not only the expression dynamic of single TF but they also consider TF gene families in their whole. This approach takes into consideration the functional redundancy that can be shared between members of the same TF gene family and identify TF gene families predominantly expressed at specific developmental stages. An interesting result described in the paper is the prediction of Transcription Factor Binding Sites (TFBSs) and their cognate TF. The large number of transcriptomes that are analyzed in the paper and the establishment of stringent selection criteria are used to infer sets of strongly coexpressed genes and to predict TFBSs. Combining different methods, Chun-Ping and collaborators identify 253 new TF-TFBS pairs in maize. Altogether, the results described contribute to better understand the regulatory circuit that occurs during maize leaf development. Raffaella Battaglia, 2015

6/2015 Raffaella Battaglia
Li, C et al. 2015. Plant Cell 27:532-545
   Genome-Wide Characterization of cis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework of Opaque2 in Maize

opaque2 (o2) mutant maize kernels have been described few decades ago due to their higher lysine content compared to wild-type kernels. The phenotype is due to a mutation in a bZIP transcription factor; a modified version of the o2 mutation later led to the development of Quality protein maize (QPM) with important repercussion for the production of high-yield and high-protein maize. In this paper, Chaobin and collaborators combine genome-wide approaches as RNA-seq and ChiP-seq to i) compare the transcriptome of o2 maize endosperm with wild-type endosperm and ii) identify direct target genes of the O2 protein. O2 appears to be a key factor in plant metabolism controlling the transcription of different zeine genes, genes involved in endosperm carbon portioning, stress resistance genes and transcription factors. Interestingly, lncRNAs are indirectly activated by O2. Furthermore, novel O2 binding sites are identified by the authors. Raffaella Battaglia, 2015

6/2015 Michael Gore
Lu, F, et al. 2015. Nature. 6:6914
   High-resolution genetic mapping of maize pan-genome sequence anchors

Data can be downloaded here: here.

Genotyping by sequencing (GBS), a current standard genotyping platform for maize, is a reduced-representation approach, sequencing at high density the subset of low-copy genomic regions tagged by cut sites of a selected restriction enzyme (Elshire et al. 2011). With the plummeting of DNA sequencing costs, ultra-high density genotyping has now become a reality and can even enable assembly of pan-genomes. However, extensive structural variation is present in maize, including transposable and other repetitive elements, copy number variation (CNV), presence/absence variation (PAV), inversion, and translocation. These variable expansions, contractions, and rearrangements complicate alignment of diverse whole-genome sequences into an assembled maize pan-genome, which is useful for understanding and leveraging extant variation. The study of Lu et al. (2015) marks a hinge point in maize genomics through its use of high-quality, mapped GBS sequence tags to anchor the assembly of a maize pan-genome. This study used GBS to sequence more than 14,000 maize inbred lines, resulting in 1.3 trillion bp of sequence at an average depth of 0.3 reads per site per sample. By implementing the GBS bioinformatics pipeline, ~26 million GBS tags were identified, and from these tags nearly 700,000 SNPs were identified and scored across all the lines. Then, two genetic mapping approaches (GWAS and joint-linkage mapping) were used to test for association between individual SNP genotypes and the PAV pattern of each GBS tag. In sum, ~22 million sequence tags were initially mapped to the genomic position of the SNP with which each tag showed strongest association, but ~35% were mapped to the incorrect chromosome.

As a result, machine learning (ML) models trained on uniquely aligned B73 tags (UABTs) mapped by JL, GWAS, or both were developed to predict map accuracy and identify accurately mapped tags for the selection of high-quality sequence anchors for the maize pan-genome. The application of three M5Rules ML models selected 4.4 million GBS tags with mapping accuracies lending themselves well to serving as unique sequence anchors. Illustrating the challenge of short-read sequence alignment in a complex genome such as that of maize, MiSeq paired end sequencing of 95 diverse inbreds was used to assess the accuracy of alignments for the 4.4 million tags, and estimated a 20% error rate in alignment for 150 to 300 bp reads. Notably, 26% of the selected tags were classified as PAVs, suggesting that B73 contains only ~74% of the low-copy sequence of maize. Additionally, 89% of the 1.1 million PAV tags absent from the B73 reference genome were found to be present in the genome assembly of the deeply sequenced maize inbred line, CML247. In general, PAVs were more frequently found in pericentromeric regions and showed a positive correlation with repeat density. SNPs associated with PAVs were found in additional GWAS of over 2,000 diverse inbreds to be enriched for significant associations in four agronomic traits. This finding supports a hypothesis that has driven efforts to assemble a pan-genome, that structural variation is also functional, and further suggests the high gains to be made from these efforts. Michael Allen Gore, 2015

This paper reports the deep SEQUENCING and assembly of the maize inbred CML247.

6/2015 Carolyn Rasmussen
Li, F et al. 2015. Plant Cell pp.doi: 10.1105/tpc.15.00158
   Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization

Autophagy serves to recycle components of the cytoplasm including organelles by targeting them to the vacuole for degradation thereby freeing nitrogen for other uses. This paper demonstrates the important role of autophagy for nitrogen remobilization during seed production. RNA-sequencing demonstrated that autophagy genes are ubiquitously expressed but upregulated in mature maize leaves and roots and endosperm suggesting that proteins are being recycled upon senescence. Coexpression analysis suggested that certain autophagy pathway isoforms may work together in specific tissue types. Annotation of the authophagy pathway revealed several single copy genes including autophagy-related 12 (atg12) and 2 Uniform-Mu insertions provided mutants in atg12. ATG12 is a ubiquitin fold protein that acts together with ATG5 and ATG 16 to ligate ATG8 to the lipid phophatidylethanolamine which aids in trafficking autophagosomes to the vacuole. atg12 mutants show reduced ATG8 lipidation and fail to accumulate YFP-ATG8 in autophagic bodies even under nitrogen or fixed-carbon limitation. Plants lacking ATG12 have reduced seed yield in nitrogen sufficient conditions and premature leaf senescence, and more severe phenotypes during nitrogen limitation. The reduction in seed yield is due to defects in nitrogen remobilization efficiency to the seeds in atg12 mutants demonstrated by nitrogen partitioning assays. Together, these results demonstrate the important role of autophagy in nitrogen remobilization during development and seed production. Carolyn G. Rasmussen, 2015

6/2015 Weibin Song
Xing, A, et al. 2015. J Exp Bot. 0:doi: 10.1093/jxb/erv182
   A rare SNP mutation in Brachytic2 moderately reduces plant height and increases yield potential in maize

The plant height is known as an important trait during maize breeding progress, many QTLs and several mutants corresponding to the plant height have been reported. But few QTL has been cloned and functional studied. In the present study, Xing et al. reported the fine mapping and cloning of the major plant height QTL, qph1, using a RIL population and the near-isogenic lines. The qph1 was narrowed down to a 1.6 kb interval on maize chromosome 1. In that interval, a mutant site was fund in the coding sequence of the Brachytic2 gene that has been characterized for ten more years. The naturally occurring rare SNP in qph1 resulted in an amino acid substitution and was validated as the causative mutation. Association analysis among 527 inbred lines using the SNP showed that the mutant site produced a rare allele. QPH1 protein is located in the plasma membrane and polar auxin transport is impaired in the short near-isogenic line RIL88 (qph1). Allelism testing showed that the SNP variant in qph1 reduces longitudinal cell number and decreases plant height by 20% in RIL88 (qph1) compared to RIL88 (QPH1), and is milder than known br2 mutant alleles. The effect of qph1 on plant height is significant and has no or a slight influence on yield in four F2 backgrounds and in six pairs of single-cross hybrids. Moreover, qph1 could reduce plant height when heterozygous, allowing it to be easily employed in maize breeding. Overall, the new allele with less-severe effect on the plant height has great potential in maize genetic improvement. Weibin Song, 2015

5/2015 Weibin Song
Li, P et al. 2015. J Exp Bot 0:doi: 10.1093/jxb/erv127
   A genetic relationship between nitrogen use efficiency and seedling root traits in maize as revealed by QTL analysis

Root system architecture (RSA) is characterized by their roles in anchorage and absorption of nutrients and water, and ability to respond dynamically to the soil environment. Many studies have demonstrated the ability of maize to alter growth patterns in order to explore for and utilize nutrient such as nitrogen. But the genetic relationship between RSA and nitrogen use efficiency (NUE) traits remains largely unkown. In this study, the authors investigated the genetic basis of RSA and NUE traits in maize using a recombination inbred line population that was derived from two lines contrasted for both RSA and nitrogen use efficiency traits. The authors performed the QTL identification at the conditions of high-nitrogen and low-nitrogen, and totally 10 NUE- and 9 RSA-related traits were evaluated in four field environments and three hydroponic experiments, respectively. Based on the phenotypic analysis, the nitrogen uptake efficiency (NupE) had significant phenotypic correlations with RSA, especially for the traits of seminal roots and crown roots, the main components of the mature root structure. Further QTL analysis indicated that 331 quantitative trait loci (QTLs) were detected. Among these QTLs, five important QTLs clusters at the chromosomal regions bin1.04, 2.04, 3.04, 3.05/3.06, and 6.07/6.08 were found in which QTLs for both traits had favourable effects from alleles coming from the large-rooted and high-NupE parent. Some of the QTL with positive effect will increase the grain yield using the advanced backcross-derived lines. Generally, understanding the genetic basement will contribute the genetic improvement of the root structure and the nitrogen utilization. The larger effect QTL that identified in the present study could be used as candidates for further cloning the RSA and NUE related genes. Weibin Song, 2015

5/2015 Michael Gore
Chung-Ju Rachel Wang
Rodgers-Melnick, E et al. 2015. Proc Natl Acad Sci, USA 112:3823-3828
   Recombination in diverse maize is stable, predictable, and associated with genetic load

Within the context of crop improvement, recombination is the evolutionary engine of plant breeding populations, providing new allelic combinations on which artificial selection can act for fixation in or purging from the population. The efficiency of selection is especially increased when recombination breaks up associations between favorable and deleterious variants. With this in mind, Rogers-Melnick et al. (2015) explored the highly variable landscape of recombination in the US and Chinese (CN) maize nested association mapping (NAM) populations, with each NAM population consisting of multiple biparental families connected through a common female parent (B73 for US, Huangzaosi for CN). Through analysis of genotyping-by-sequencing (GBS) data, 136,000 cross-over events were identified at high resolution and their frequencies found to be highly predictable between populations and across families. Notably, cross-over rate was found to be negatively associated with CpG methylation, and repeat content, resulting in suppression of cross-over events in pericentromeric regions and enrichment in subtelomeric regions. In some families, recombination was found to be suppressed over non-pericentromeric regions spanning one or more megabases; this pattern was tentatively attributed to inversions through examination of maize/sorghum synteny. Through a Bayesian modeling approach, recombination hotspots (i.e., intervals of crossover enrichment) were identified, ranging in size from 1 to 30 kb that were highly conserved between both NAM populations. Relative to control regions, these hotspots showed distinct patterns of higher prevalence of hypomethylation as well as higher mean GC content and GC-biased gene conversion. Genomic evolutionary rate profiling (GERP), which infers the history of purifying selection acting on a nucleotide site from a multi-species comparison, revealed that hotspots had a lower genetic load (fewer deleterious alleles) than the genome-wide average. The present constraints of recombination severely limit the purging of deleterious alleles, which perhaps can only be efficiently conducted through breeding with technologies that can increase the global recombination rate (i.e., QTL or transgenes for increased recombination rate) and edit the genome for both nucleotide and methylation patterns. Michael Gore, 2015

Maize is notable for its genetic diversity within the species as the average genetic distance between two inbred lines exceeds that between human and chimpanzees. These allelic variations provide a large number of allelic combinations for breeding. On the other hand, shuffling linkage groups to purge deleterious alleles or to combine all the preferable genes requires meiotic recombination. It has been known that recombination can vary over 1000-fold across the maize genome. In this study, Rodgers-Melnick et al analyzed markers by genotyping-by-sequencing (GBS) within US and Chinese maize nested association mapping (NAM) populations to map a total of 136,000 recombination breakpoints- where crossovers occurred. They found that the pattern of crossovers is highly predictable, for example, CpG methylation has a strong negative relationship with the crossover density. By comprising crossover sites among lines, recombination hotspots were identified and found to be historically stable across two diverse sets of maize germplasm. They also found that the regions of the maize genome with the lowest recombination rates accumulate the largest number of deleterious alleles. This finding suggested that these portions of the maize genome may harbor undesirable genes that will be difficult to be removed by conventional breeding techniques. Rachael Chung-Ju Wang, 2015

5/2015 Raffaella Battaglia
Yu, CP, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1500605112
   Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

The gene regulatory network that controls maize leaf development is still not well understood. This knowledge may be useful for developing C3 crops to perform C4 photosynthesis for enhanced yields in a long run. In this study, Yu et al studied 22 transcriptomes of developing maize leave from dry seeds to 192 hours post imbibition. Through coexpression and differential gene expression analysis, authors identified functional transitions with molecular signatures during leaf development. Interestingly, authors analyzed expressions of transcription factors (TFs) among 22 samples, and highlighted the key TF families involved in developmental and physiological processes. More significantly, authors used maize genomic sequences and transcriptomic data or used the known TFs and its transcription factor binding sites (TFBS) in rice and Arabidopsis to predict maize TF-TFBS pairs during leaf development. In total, about 1300 novel TFBSs and 253 new TF-TFBS pairs were identified in maize. This dataset will serve as the foundation for a systems biology approach to the understanding of regulatory network involved in maize leaf development. Rachel Wang, 2015

Chun-Ping and colleagues use an extensive data set to finely describe the transcriptional changes that occur during leaf development in maize. The authors analyze 22 transcriptomes with a time span from hour 0 (dry seeds, T000) to 192 h post imbibition (T192). The possibility of having this large dataset allows to precisely identify genes that are coregulated and involved in the same biological processes. 30 co-expressed modules are divide into three stages and different criteria are used to define Differentially Expressed Genes (DEGs). Focusing on Transcription Factors (TFs), the authors describe not only the expression dynamic of single TF but they also consider TF gene families in their whole. This approach takes into consideration the functional redundancy that can be shared between members of the same TF gene family and identify TF gene families predominantly expressed at specific developmental stages. An interesting result described in the paper is the prediction of Transcription Factor Binding Sites (TFBSs) and their cognate TF. The large number of transcriptomes that are analyzed in the paper and the establishment of stringent selection criteria are used to infer sets of strongly coexpressed genes and to predict TFBSs. Combining different methods, Chun-Ping and collaborators identify 253 new TF-TFBS pairs in maize. Altogether, the results described contribute to better understand the regulatory circuit that occurs during maize leaf development. Raffaella Battaglia, 2015

5/2015 Carolyn Rasmussen
Chettoor, AM; Evans, MMS. 2015. Frontiers Plant Sci. 0:doi: 10.3389/fpls.2015.00187
   Correlation between a loss of auxin signaling and a loss of proliferation in maize antipodal cells

Within the female gametophyte (embryo sac), the antipodal cells are likely to produce and distribute auxin in the ovule. The embryo sac contains several different cells including the egg cell, synergids, central cell and the antipodal cells. The authors mined data from RNA sequencing of embryo sac enriched samples and compared them to ovule samples in which the embryo sac was removed. The embryo sac enriched samples have higher mRNA expression levels of multiple components of the auxin biosynthesis, transport and signaling pathways compared to the surrounding ovule. The phylogenetic tree of several families was displayed with over represented mRNAs highlighted, a useful way to visualize the relationship between gene relationship and expression patterns. In an interesting comparison, the Auxin Response Family (ARF) gene family was displayed with both ARF family members targeted by artificial microRNAs that caused embryo sac development defects in Arabidopsis thaliana, with those overrepresented in the embryo sac in maize. One class of ARFs, Class II, was most overrepresented in maize embryo sacs, but was not targeted by the artificial microRNAs in A. thaliana, making correlations between expression and previous functional analysis difficult. To determine which cells within the embryo sac were responding to auxin, PIN1a-YFP, an auxin efflux transporter and pDR5-RFP, an auxin responsive promoter fused to RFP, were used to determine which cells contributed to the increased mRNA expression of auxin in the embryo sac. Although the PIN1a-YFP patterns were variable, they were concentrated with the antipodal cells as was the pDR5-RFP signal. Finally, in a dominant mutant that alters both embryo sac development and abaxial leaf polarity called Laxmidrib1-O (Lxm1), PIN1a-YFP and pDR5-RFP expression was reduced in the antipodal cells as was the number of antipodal cells. Intriguingly, the expression of pDR5-RFP was also lower in the nucellus, part of the ovule, in Lxm1 suggesting that the source of auxin for the nucellus may come from the antipodal cells. This is an important paper because little is known about the function of antipodal cells and their persistence during development within the grasses. The authors propose that auxin may be playing a role in antipodal cell proliferation and potentially that antipodal cells may promote proper seed development. Carolyn Rasmussen, 2015

4/2015 Michael Gore
Wallace, JG, et al. 2014. PLoS Genetics. 10:e1004845
   Association mapping across numerous traits reveals patterns of functional variation in maize

One of the more difficult challenges facing biology in the 21st century is pinpointing the causative variants responsible for natural phenotypic variation in organisms. The tremendous genetic and phenotypic diversity of maize complemented by its extensive genetic and genomic toolbox make it a powerful model system for the genetic dissection of complex trait variation. In this light, Wallace et al. (2014) conducted a genome-wide association study (GWAS) in the U.S. maize nested association mapping (NAM) panel for 41 different phenotypes that covered a range of genetic complexity. Through forward-regression GWAS with the high-resolution HapMap v. 1 and 2 data set [28.9 million single-nucleotide polymorphisms (SNPs) and nearly 800,000 copy-number variants (CNVs)], remarkably only 4,484 SNPs and 318 CNVs were found to be significantly associated with at least one of the traits tested. The strongest class enrichment was for genic SNPs and CNVs, especially synonymous SNPs and large CNVs. However, almost 70% of the ~4800 variants resided outside of annotated genes (gene-proximal, within 5kb of a gene; or intergenic, more than 5 kb away from a gene) in the likely vicinity of promoters and regulatory elements. This study also found that minor allele frequency and standardized effect size generally had an inverse relationship that was consistent across variant classes. That is, rarer, larger-effect variants from the intergenic class tended to explain a smaller amount of unique variance in each trait than did more common, smaller-effect variants from the genic and gene-proximal classes. Genes related to regulatory activity and those that had a paralog were found to be enriched for GWAS associations, whereas genes with low expression values and involvement in core metabolic functions showed slight depletion even though 14 metabolite traits were included in the analysis. While it remains a major challenge to identify the causative variants controlling a phenotype, the results of this study suggest that expanding the variant search space to include the still-inadequately annotated non-genic regions of the complex maize genome is needed. Michael Gore, 2015

4/2015 Carolyn Rasmussen
Zoschke, R; Barkan, A. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1424655112
   Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

In this study, the authors use a large-scale "ribosome profiling" approach to clarify how plastid encoded proteins are targeted to the thylakoid membrane. Plastid encoded proteins are targeted to the thylakoid membrane via two distinct processes that depend strongly on the structure of the protein. When the transmembrane domain is located within 80 amino acids of the end of the protein, the protein is posttranslationally targeted to the thylakoid membrane. In contrast, if the transmembrane domain or signal sequence is further than 80 amino acids from the stop codon, it is targeted to the membrane as it is being translated (cotranslationally targeted). The method used to deduce this rule for thylakoid membrane targeting is called ribosome profiling. Maize leaf mRNAs are separated into soluble and membrane fractions, then treated with ribonucleases. If the mRNA is inside the ribosome, it is protected from degradation by ribonucleases. The small, protected fragments of the mRNA are called the ribosome footprint, and they were hybridized to a tiling microarray to determine their sequence and location. If ribosome footprints were partitioned into the membrane fraction, the newly formed peptide was inserted into the membrane as it was translated. Two exceptional cases were identified. The first exceptional case is the only protein that contains a chloroplast signal peptide, PetA. In this case, the signal peptide, not the transmembrane domain, is determinant for co-translational membrane targeting. The other case is the only plastid-encoded protein that localizes to the inner envelope membrane, CemA. Although the mechanism is unknown, the transmembrane domains of this protein do not target the mRNA to the thylakoid membrane, suggesting that the lysine rich CemA specific sequence prevents thylakoid membrane insertion. After global analysis, the rules for plastid encoded protein targeting to the thylakoid membrane were identified and it is likely that these rules can be extended to bacterial proteins. Carolyn G. Rasmussen, 2015

4/2015 Chung-Ju Rachel Wang
Zhai, J et al. 2015. Proc Natl Acad Sci, USA 112:3146-3151
   Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers

In this study, Zhai et al. found that two distinct classes of phased small-interfering RNAs (phasiRNAs) are transcribed during maize anther development. By small RNA profiling of 10 stages of maize anthers, authors identified that 21-nt phasiRNAs from 463 loci appear abruptly after germinal and somatic cell specification, whereas 24-nt phasiRNAs from 176 loci accumulate during meiosis. Interestingly, in situ hybridization and sequencing of RNA from several anther developmental mutants demonstrated that 21-nt phasiRNAs biogenesis triggered by miR2118 requires a functional epidermis, and 21-nt siRNAs then likely move to all the cell layers of anthers. In contrast, miR2775 triggers the biogenesis of 24-nt phasiRNAs, and 24-nt siRNA all accumulate preferentially in tapetum and meiocytes. This finding revealed an interesting spatial-temporal control of two classes of phased siRNAs. Their particular abundance in reproductive organs resembles the piRNA in mammals. piRNAs are a conserved class of small RNAs that are found during male reproductive stages in animals. It had been notable that piRNAs are absent in plants, yet this finding suggests a putative convergent evolution to produce small RNAs in reproductive organs. Rachel Chung-Ju Wang, 2015

4/2015 Weibin Song
Yi, G; Neelakandan, AK; Gontarek, BC; Vollbrecht, E; Becraft, P. 2015. Plant Physiol. 167:443-456
   The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm cell patterning and differentiation

In this study, the authors showed us the cloning and functional analysis of the two unlinked genes encoded by the INDETERMINATE domain transcription facor, and the two genes are homologous genes distributed on chromosome 2 and 10, respectively. Knocking down or knocking out either gene will show naked endosperm (nkd) phenotype. Phenotypic analysis revealed that the aleurone cell differentiation was disrupted in the nkd mutant, and also resulted in reduced filling in the mutant seed. Positional cloning method was used to isolate the two genes, and additional alleles were found to confirm that the candidates were corresponded to nkd1 and nkd2. Expressing patterns of the two genes showed that the NKD transcripts accumulated higher around 11 to 16 day after pollination. Subcelular localization showed that the fused protein of NKD-GFP was found in the nuclei of the onion. Finally, the data presented by Yi and colleagues provided us new insight into understanding the aleurone cell differentiation in maize. Weibin Song, 2015

4/2015 Raffaella Battaglia
Zhan, J, et al. 2015. Plant Cell. 0:513-531
   RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

In this paper the Authors describe the molecular networks that control cell differentiation in specific filial and maternal compartments of the maize kernel. The expression profile of cells dissected from Aleurone (AL), Basal Endosperm Transfer Layer (BETL), Embryo-Surrounding Region (ESR), Conducting Zone (CZ), Central Starchy Endosperm (CSE), Embryo, Nucellus, Placento-Chalazal region, pericarp and vascular region of the pedicel at 8 Days After Pollination (DAP) allowed to identify compartments-specific genes. These results are the starting point to define modules of co-expressed genes and gene regulatory networks (GRNs) that regulate kernel differentiation both temporally and spatially. The statistical analysis of RNA-seq data indicate that at least 18 coexpression modules (M1- M18) can be described in the developing kernel at 8 DAP. Focusing the attention on endosperm, the Authors identify cis-regulatory elements enriched in the promoter region of genes belonging to each coexpressed module. Interestingly, within a BETL coexpressed module, a large subset of genes are direct target of the Myb-Related Protein-1 (MRP-1) factor. As a whole, the data presented by Zhan and colleagues represent a clear dissection of the network occurring in a model system, as the developing maize endosperm, which also represents an important resource for food, feed and raw material. Raffaella Battaglia, 2015

3/2015 Carolyn Rasmussen
Facette, MR et al. 2015. Nature Plants 0:Article number: 14024
   The SCAR/WAVE complex polarizes PAN receptors and promotes division asymmetry in maize

This paper identified the dependence of the leucine-rich repeat receptor-like kinases PANGLOSS1 (PAN1) and PAN2 on one of the regulators of branched actin nucleation called the SCAR/WAVE regulatory complex (WRC) in an asymmetric division leading to the formation of the stomata in maize. The stomatal complex is formed through the development of a guard cell bordered on two sides by two small triangle shaped subsidiary cells. The subsidiary cells are formed by an asymmetric division of the subsidiary mother cell (SMC), which is preceded by actin accumulation and nuclear movement toward the guard mother cell (GMC). In maize, it was previously shown that one member of the WRC, called BRICK1 because its pavement cells lacked crenulations and resembled bricks, also had an role in SMC divisions. Other mutants (brk2 and brk3) with similar defects in both pavement cell crenulation and subsidiary cell division were previously characterized, but their genetic identity was previously unknown. This paper identified maize BRK3 as a component of the WRC, and further identified a complex containing all five components of the WRC by co-immunoprecipitation followed by mass spectrometry. Next, the genetic relationship between the WRC and PAN1 and PAN2 was analyzed When mutants in the WRC, brk1 and brk3, are combined with pan1 or pan2 mutants, they have a synergistic effect on subsidiary cell development (up to ~90% abnormal) suggesting non-overlapping or convergent roles in subsidiary cell development. Using the developmental gradient of the maize leaf, a clear relationship between the GMC length and the developmental stages of the SMC, and localization of fluorescently tagged proteins in mutants, the authors identified epistasis relationships between the WRC, PAN1, PAN2, the monomeric small GTPase RHO GTPASE OF PLANTS (ROPs), as well as actin patch formation and nuclear polarization. After formation of the guard mother cell, BRK1 (which is a proxy for the entire WRC) localizes first to the SMC and indirectly recruits PAN1 and PAN2 to the SMC; PAN1 and PAN2 failed to localize to the SMC in either brk1 or brk3 mutants. This result is significant because it suggests branched actin networks polarize PAN2 and PAN1. Then, as previously described, PAN1 directly recruits ROP2 to the SMC and activates it leading finally to actin patch and nuclear polarization. Based on these observations the authors suggest a model where the SCAR complex first is responsible for polarizing PAN receptors, and then later PAN receptors activate SCAR to stimulate actin patch formation. Carolyn Rasmussen, 2015.

3/2015 Weibin Song
Zuo, W et al. 2015. Nature Genetics 47:151-157
   A maize wall-associated kinase confers quantitative resistance to head smut

Head smut is a systemic fungal disease caused by S. reilianum that occurs in most maize-growing areas and causes tremendous loss of yield. In this study, Zuo et al isolated a major QTL, qHSR1, corresponding to the resistance to maize head smut using a classical strategy of map-based cloning. Sequencing and transgenic complementation demonstrated that the resistance gene encoding a receptor-like kinase in maize named ZmWAK (wall-associated kinase) . The functions of WAK and WAK-like proteins have been investigated deeply in other plants such as Arabidopsis, and these genes mainly involved in plant development, signaling perception and transduction and including plant defense. ZmWAK was highly expressed in the mesocotyl of seedlings where it arrested biotrophic growth of the endophytic S. reilianum. Domestication analysis of ZmWAK, including the spread in maize germplasm has been also performed. Taken together, these results provide us both a model for resistance QTL cloning and a new strategy to control head smut for maize breeders. Weibin Song, 2015

3/2015 Michael Gore
Technow, F, et al. 2014. Genetics. 197:1343-1355
   Genome properties and prospects of genomic prediction of hybrid performance in a breeding program of maize

Commercial hybrid maize breeding has been traditionally reliant on per se and testcross performance results to select superior inbred line parents, suspending the evaluation of experimental hybrids for ultimately the final stage of the breeding cycle. Genomic prediction of hybrid performance when combined with contemporary advances in double haploid, genotyping, and phenotyping technologies finally offers the potential to identify superior single-cross hybrids at the early stages of the breeding pipeline. As perhaps a glimpse into the not-so-distant future of breeding maize hybrids, Technow et al. (2014) analyzed genotypic and phenotypic data collected from 1,254 single-cross maize hybrids built on Dent x Flint heterotic patterns that had been in part evaluated over 14 years and 20 locations in Southern Germany. Statistical examination of the genome-wide SNP marker data revealed a high concordance in linkage phases but major differences in allele frequencies between the Flint and Dent heterotic groups at pericentromeric regions of maize chromosomes. It is at these recombinationally suppressed pericentromeric regions where the Hill-Robertson effect is likely to be strongest. Such findings support differential fixation of alleles due to pseudo-overdominance - repulsion phase linkage between QTL alleles - at pericentromeric regions as a major contributor to the genetic basis of heterosis. Genomic prediction of grain yield and moisture with two different statistical models was highest for untested hybrids when both parents were parents of other hybrids in the training set, and in contrast, lowest when neither parent contributed to training set hybrids. How best to optimize the size and composition of the training set, particularly in relation to population and family structures, is still an ongoing research question. As these findings illustrate, identifying the best hybrid - a pursuit initiated more than 100 years ago by G. H. Shull - now has a better chance of becoming an early-stage venture. Michael Gore, 2015

3/2015 Chung-Ju Rachel Wang
Pautler, M, et al. 2015. Plant Cell. 0:doi 10.1105/tpc.114.132506
   FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize

The stem cells in shoot apical meristem (SAM) are capable of generating founder cells for organ initiation and self-renewing to maintain its own cell numbers. The balance between self-renewal of central stem cells and organ initiation from peripheral cells is controlled by dynamic, complex signaling networks, for example the well-characterized CLV-WUS negative feedback pathway. In this study published by Pautler et al, a fasciated ear mutant, fea4 was isolated. Unlike most of previously identified fasciated ear genes, such as fea2, td1 and ct2, which are directly involved in the CLV pathway, FEA4 acts in parallel to the CLV pathway. FEA4 encodes a bZIP transcription factor, as a negative regulator of meristem size. Its RNA is present in the peripheral zone of the SAM, and in the vasculature of young leaves it is excluded from the stem cell niche. Both double mutant analysis and transcriptome profiling suggested that FEA4 is not directly involved in the CLV pathway. Finally, ChIP-seq and RNA-seq experiments revealed that FEA4 may regulate gene expression that are involved in auxin response pathway and other homeobox transcription factors to accelerate differentiation in the peripheral zone. Rachel Wang, 2015.

3/2015 Raffaella Battaglia
Yang, F, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.114.130393
   A maize glutaredoxin gene, abphyl2, regulates shoot meristem size and phyllotaxy

The Authors describe a yet unknown mechanism controlling meristem size and phyllotaxy in maize. The identification of the new dominant maize mutant Aberrant phyllotaxy2 (Abph2) allowed Yang and colleagues to demonstrate that a GLUTAREDOXIN (GRX) gene plays a role in the regulation of SAM size and phyllotaxy. In the Abph2 genetic background, an active copy of the MALE STERILE CONVERTED ANTHER1 (MSCA1) gene appeared to be transposed in the Abph2 locus and misexpressed during embryo development. As a result, mutant plants showed an enlarged meristem and a decussated phyllotaxy. MSCA1 encodes a GLUTAREDOXIN protein, a redox regulator, proposed to post transcriptionally regulate transcription factors. Using genetic approaches and molecular analysis, the Authors indicate the FASCIATED EAR4 (FEA4) factor as a candidate target controlled by MSCA1. The MSCA1 gene has been already described as a regulator of anther development in maize, the fact that a GRX protein is involved in SAM size determination and phyllotaxy was presumably masked by functional redundancy with two close homologs identified on the maize genome. It is now challenging to understand how hormones and redox signals crosstalk to determine SAM size and phyllotaxy. Raffaella Battaglia, 2015

2/2015 Raffaella Battaglia
Li, XJ, et al. 2014. Plant J. 79:797-809
   Small kernel1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize and rice

In this study, the Li et colleagues describe the role of C to U editing in mitochondria transcripts. The characterization of the maize small kernel 1 (smk1) mutant allows the Authors to correlate mitochondrial complex I assembly, seed development and nad7-836 transcript editing. Smk1 is a nuclear gene encoding a mitochondrion-targeted PPR-E subclass protein that is required to specifically edit the mitochondrial nad7-836 transcript and to create a leucine codon at position 279; a loss of editing in mutant plants leaves a proline codon. This gene is ubiquitously expressed, nevertheless mutations in Smk1 mainly affect kernel formation; embryo and endosperm development is delayed with approximately 90% of the mutant kernels being completely lethal. Analysis of the mitochondrial protein complexes and morphological studies reveal that the loss of nad7-836 editing in the smk1 mutant disrupts complex-I assembly thus leading to abnormal mitochondrial biogenesis. Interestingly, specific protein domains within the PPR-E subclass proteins are highly conserved across species. Focusing on the orthologous rice Os_Smk1 gene, the Authors highlight the functional conservation between the maize and rice Smk1 genes showing that demonstrate that the nad7-836 editing function is critical to embryo and endosperm development in both species. Raffaela Battaglia, 2015

2/2015 Chung-Ju Rachel Wang
Chuck, GS; Brown, PJ; Meeley, RB; Hake, S. 2014. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1407401112
   Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordia initiation

The number of lateral primordia made by the male and female inflorescences of maize is a major determinant of yield, since it dictates tassel branch number (TBM) and ear row number (ERN). In this study, Chuck et al identified SBP-box transcription factors, unbranched2 (ub2) and unbranched3 (ub3) that share similarity with tasselsheath4 (tsh4), a gene responsible for repression of leaf primordia in maize inflorescences. Double mutants of ub2 and ub3 display a decrease in TBM and an increase in ERN. SEM on tassels further showed that many extra tows of spikelet pair meristems are initiated with extra leaves at the base of the tassel. Taken together, these results suggest that ub2 and ub3 function together to limit the rate of lateral primordia initiation in the wild-type. Immunolocalization of UB2 and UB3 proteins found accumulation throughout the meristem but absence from the central domain of the meristem where cells regenerate. Interestingly, the ub3 locus is tightly linked to QTL for ERN and TBM in both the nested association mapping (NAM) and intermated B73 by Mo17 (IBM) populations of maize recombinant inbreds, suggesting this gene may be agronomically important. Rachel Wang, 2015.

2/2015 Carolyn Rasmussen
Johnston, R, et al. 2014. Plant Cell. 0:doi: 10.1105/tpc.114.132688
   Transcriptomic analyses indicate that maize ligule development recapitulates gene expression patterns that occur during lateral organ initiation

A global analysis of the transcripts was performed to identify genes that are specifically enriched or underrepresented found in the developing ligule. Laser-microdissection, in which a specific set of cells is removed, was used to isolate cells from developing ligule and surrounding blade and sheath and followed by RNA-sequencing. As a control, equivalent tissue was also dissected from a mutant that does not form a ligule, liguleless1 (lg1). A set of 34 genes with higher transcript levels in the developing ligule also had reduced transcript abundance in the lg1 mutant suggesting that these transcripts are specific for the ligule. Intriguingly, many of the genes that had high transcript levels in the developing ligule were transcription factors that have been previously identified in lateral organ patterning or leaf initiation such as narrow sheath 1 and several Class III Homoedomain leucine zipper (HD-ZIPIII) genes. Boundary specification genes such as the maize homologs of CUP-SHAPED COTEYLEDON2 and BLADE-ON-PETIOLE1/2 had enriched transcript levels in developing ligules. When in situ hybridization was used to confirm the expression patterns, these transcripts and others were observed not only in developing ligules, but also at lateral organ boundaries. Partners of KNOX homeobox transcription factors, BEL transcription factors 12 and 14, are also expressed in the developing ligule. A model is proposed where auxin from the developing blade restricts homeobox transcription factors to the developing ligule and sheath to specify the blade-sheath boundary. Carolyn Rasmussen, 2015

2/2015 Michael Gore
Rincent, R et al. 2012. Genetics 192:715-728
   Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.)

Genomic selection is a breeding approach that has shown promise in plants to accelerate the breeding cycle by enhancing genetic gain per unit of time through the early selection of nonphenotyped individuals (selection candidates or validation set) that show favorable genomic signatures for targeted traits. Essentially, a set of molecular markers is used to predict breeding values for individuals based only on their marker genotypes. The prediction of breeding values is founded on a statistical model that has been calibrated (or trained) on the phenotypes and genotypes of reference individuals (reference population or calibration set). Importantly, the size and composition of the calibration set are some of the critical parameters that directly impact the reliability of predictions (the correlation between predicted and true breeding values). In that light, Rincent et al. (2014) tested several methods to maximize the reliability of genomic predictions through optimally selecting individuals to comprise the calibration set based on marker data alone. These methods were tested on two independent maize diversity panels (one Dent and one Flint) that had been genotyped with a 50k SNP array and phenotyped for three traits (male flowering time, plant biomass, and dry matter content) with differing levels of heritability. Specifically, the performance of two metrics used to select calibration sets for optimized genomic prediction reliability were compared. The generalized coefficient of determination (CD) accounts both for error variances of the marker-based predictions (PEV) and for the potential reduction in genetic variance due to relatedness (i.e., prevents the selection of very closely related individuals). An optimized selection algorithm based on the CD mean was found to impart higher reliabilities for the three traits in both panels across a number of calibration set sizes compared to use of the PEV mean alone, which does not penalize for high relatedness. These results suggest that the CD mean algorithm can be used to efficiently optimize the composition of calibration sets, allowing for an increase in genomic prediction reliability with a concomitant decrease in the number of reference individuals needed to be phenotyped. Michael Gore, 2015

1/2015 Chung-Ju Rachel Wang
Gent, JI, et al. 2014. Plant Cell. 0:doi: 10.1105/tpc.114.130427
   Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation

The maize genome is notable for its numerous transposons and repeat sequences, and those regions are often tightly packed and stained densely under microscopes, named as heterochromatin. Heterochromatin formation is implicated in gene silencing with presence of specific chromatin modifications, such as histone H3K9me2 or H3K27me2. Studies in yeast have shown that RNA-directed DNA methylation (RdDM) pathway is involved in heterochromatin formation; however, multiple studies in plant genomes suggested that RdDM is not a uniform feature of heterochromatin. The relationship between RdDM and heterochromatin in plants is unclear. In this study, Gent et al compared several heterochromatic features, including H3K9me2 and H3K27me2, chromatin accessibility, DNA methylation and small RNAs in maize wild type as well as two mutants affecting DNA methylation, one functions independently of RdDM and the other is a key component of RdDM. Their results revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but lacks RdDM. The minority of the genome marked by RdDM appeared more similar to euchromatin than to heterochromatin. This data indicated that heterochromatin differs fundamentally from RdDM-targeted chromatin. Authors further proposed that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production. Rachel Wang 2015.

1/2015 Carolyn Rasmussen
Thompson, BE et al. 2014. Plant Cell 26:4702-4717
   The dicer-like1 homolog fuzzy tassel is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize

In this study, fuzzy tassel was identified as a partial loss of function dicer-like1 mutant in maize. The dcl1-fzt mutant was caused by a S-to-N substitution in the RNAse IIIa domain. Not surprisingly, dcl-1 loss-of-function alleles are embryo lethal, whereas those with non-silent amino acid substitutions in the helicase domain were morphologically normal. Pleotropic phenotypes of dcl1-fzt mutants include disordered inflorescence architecture, sex determination defects, short stature and narrow leaves. The mutant phenotypes appear to be caused by reduction in microRNA (miRNA) levels, which is caused by failure to appropriately process many but not all miRNA precursors. An elegant aspect of this study is the analysis of phenotypes based on the relative reduction in levels of miRNAs known to alter developmental programs. Strong defects in meristem determinacy were correlated with significant reductions (>25-fold) in the levels of miR172e/ts4. miR172e has already been implicated in regulating meristem determinacy through analysis of the tasselsheath4 mutant. Another intriguing result was that, dependent on inbred background, the phase change (whereby juvenile leaves transition into adult leaves) was either delayed or faster in the dcl1-fzt mutant compared to wild-type siblings. This is discussed in the context of relative levels of the opposing activities of two miRNAs miR156 and miR172 on phase changes. Carolyn Rasmussen, 2015.

1/2015 Michael Gore
Owens, BF, et al. 2014. Genetics. 198:1699-1716
   A foundation for provitamin a biofortification of maize: Genome-wide association and genomic prediction models of carotenoid levels

A genome-wide association study and pathway-level analysis were carried out for 24 individual and derived carotenoid traits, permitting the detection of four major-effect loci including novel associations for zep1 (zeaxanthin epoxidase) and lut1 (a cytochrome P450 required for carotenoid epsilon-ring hydroxylation) in maize. These combined approaches ascribed maize paralogs to various enzymatic steps in the carotenoid and isoprenoid biosynthesis pathways that were previously only characterized by model species. In addition, it was demonstrated that markers in the vicinity of such a priori candidate genes underlying quantitative trait loci (QTL) yielded similar prediction accuracies for carotenoid grain traits as compared to a genome-wide set of markers. Such results suggest that a small number of genes responsible for carotenoid biosynthesis and retention can be effectively employed in marker-assisted selection. Michael Allen Gore, 2015

12/2014 Andrea Gallavotti
Lewis, MW et al. 2014. Development 141:4590-4597
   Gene regulatory interactions at lateral organ boundaries in maize

The angle at which leaves are borne is an important architectural feature in plants. Modern maize varieties have been selected for upright leaves in order to increase plant density in the field. The regulation of leaf angle is determined at the junction of the sheath and the blade, whereby auricles and ligules regulate leaf angle and protect the stem, respectively. In maize, both the liguleless1 and 2 (lg1 and 2) genes are well known to regulate ligule formation and leaf angle. In this study, Lewis et al. isolated the gene that causes a previously described dominant mutant, Wavy auricle in blade1 (Wab1-R), affected in ligule, auricle and blade formation. To clone the causative gene they combined a traditional map-based cloning approach with an EMS screen for intragenic suppressors. After narrowing the map position to only two transcription factors, the lack of obvious mutations or rearrangements in the region led them to devise a genetic strategy to identify knock-outs in the dominant Wab1-R allele. The isolation of a single revertant with a point mutation in the DNA binding domain of a TCP transcriptional regulator, proved that wab1 encodes the TCP gene. This gene had been independently isolated in a previous forward genetic screen for inflorescence architecture mutants (Bai et al. 2012, PNAS 109:12225-12230). By careful genetic and molecular analysis using both dominant and revertant loss-of-function mutations, Lewis et al. determined that the normal function of wab1 is to regulate the expression of lg1 in the adaxial region at the base of the tassel branches, and that in the dominant mutant this module is activated by the overexpression of wab1 in leaves (of unknown cause). The developmental defects observed in Wab1-R are reminiscent of defects in maintaining boundaries in developing organs, such as those established between the shoot apical meristem and lateral organs (e.g. inflorescence meristem and tassel branches). Given the similar molecular and developmental program observed in the ligular region and at the junction of tassel branches, the authors propose that the ligule functions as a boundary domain in developing leaves. Andrea Gallavotti 2014

12/2014 Candice Hirsch
Stelpflug, SC et al. 2014. Genetics. 198:209-218
   Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize

Extensive phenotypic variation exists in maize and more variation is constantly being generated. One such way is through tissue cultured induced somaclonal variation. It has been well characterized in a number of plant species, including maize, that somaclonal variation exists, and that it generally results in the occurrence of unexpected phenotypes in progeny resulting from tissue culture. Understanding tissue culture induced variation is important as basic research through molecular plant breeding research can utilize tissue culture. In this study, the effect the tissue culture process has on genome-wide DNA methylation patterns of regenerated plants was investigated by generating profiles of DNA methylation in multiple regenerated plants from an inbred line. It was found that numerous regions exhibited altered DNA methylation levels, and that many of the hypomethylation events occurred at the same genomic sites across independent regenerants and cell lines. Additionally, the DNA methylation changes were in many cases heritable after self-pollination. These regions showing differential methylation may respond to more general stresses beyond that experienced during tissue culture as the regions overlapped with previously observed differentially methylated regions. This study provides important insights into not only tissue culture induced variation, but more generally, stress included variation. Candice Hirsch, 2014.

12/2014 Madelaine Bartlett
Haag, JR et al. 2014. Cell Reports 9:378-390
   Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits

Eukaryotes have three essential DNA-dependent RNA polymerases: Pol I, II, and III. Plants are distinct from other eukaryotes in possessing two additional polymerases, Pol IV and V, that synthesize RNAs involved in silencing transposons, repetitive elements, and some genes. In addition, Pol IV, and possibly Pol V, has been implicated in the epigenetic phenomenon of paramutation. Maize has a number of homologs for all of the Pol IV and Pol V components known from Arabidopsis thaliana, but the exact composition of the full twelve-subunit complexes has remained unclear. This paper describes significant advances in characterizing both Pol IV and Pol V of maize in detail. Eleven of the twelve subunits were recovered for each polymerase, and, unexpectedly, the two protein complexes are differentiated only by the identity of the largest subunits. This is not the case in A. thaliana, where there is a discriminatory Pol V-specific 5th subunit. A second interesting result is that maize has multiple subtypes of both Pol IV and Pol V that appear to be functionally distinct. This paper raises interesting questions about the historical origins of Pol IV and V, and the results hint at a surprising evolutionary fluidity in the composition of two important protein complexes. Madelaine Bartlett, 2014.

11/2014 Madelaine Bartlett
Estep, M, et al. 2014. Proc Natl Acad Sci, USA. 111:15149-54
   Allopolyploidy, diversification, and the Miocene grassland expansion

The grass tribe Andropogoneae includes not only maize, but also a number of plants of key economic importance, including sugarcane, Miscanthus, and Sorghum. This investigation into the phylogeny of the tribe has revealed an extraordinarily high level of allopolyploidy. Allopolyploids arise through genome doubling after a hybridization event between two distinct species. The investigators use gene trees todetect allopolyploids, and find evidence for allopolyploidy in at least 32% of the species sampled. It has been a matter of some debate as to whether polyploidy is a driver of diversification in plants. The position of allopolyploidy events across the dated tree generated in this study allowed the researchers involved to test the diversification hypothesis in the Andropogoneae. What they found was that although allopolyploidy does appear to be a frequent mode of speciation, the vast majority of allopolyploidy events did not result in increased diversification rates. This paper represents an interesting step forward in elucidating the evolutionary history of maize and its relatives. Madelaine Bartlett, 2014.

11/2014 Candice Hirsch
Hirsch, CN, et al. 2014. Genetics. 198:409-421
   Insights into the effects of long-term artificial selection on seed size in maize

Corn and other cereal crops are a staple food source worldwide. Seed size is an important grain yield component trait that is important in crop domestication as well as in yield improvement. Understanding the molecular mechanisms underlying cereal grain yield is important in providing a stable food source worldwide. Long-term selection experiments hold a wealth of information regarding the genetic architecture of a trait. In this study, pooled whole genome resequencing of the Krug Yellow Dent base population and populations selected for 30 cycles for small and large seed size was used to identify signatures of selection in this long-term selection experiment. In total, 94 signatures of selection were identified. Additionally a large number of copy number variation regions were identified between the extreme populations. In addition to providing insights into the genetic architecture of seed size, this study also supports a general role for non-coding sequences and copy number variation in contributing to response to phenotypic selection. Candice Hirsch, 2014.

11/2014 Andrea Gallavotti
Dooner, HK; He, L. 2014. Proc Natl Acad Sci, USA. 0:doi:10.1073/pnas.1415482111
   Polarized gene conversion at the bz locus of maize

Most of recombination events in maize are intragenic and can occur with or without crossovers. Gene conversion is the non-reciprocal transfer of information from one chromatid to another, and historically in maize it has been studied by identifying the flanking marker arrangement (usually visual markers) of intragenic recombination events. Gene conversion was shown to be the prevalent mode of recombination between dimorphic heterozygotes, that is alleles that are essentially identical but for one site. In previous studies with the bronze locus (bz) no preference in polarity of conversion, that is the tendency of markers located near one end of the gene to convert more frequently than those located at the opposite end, was observed. This contrasted with findings in fungi where conversion polarity was reported in several cases. Conversion gradients along genes are generally considered to reflect a preferential initiation site for recombination. In this study, Dooner and He used EMS and transposon excision mutagenesis to create a series of new bz alleles in the same genetic background located throughout the length of the gene to determine if preferential conversion at the proximal or distal side was indeed observed. These new alleles were tested in large diallelic crosses to test all possible heteroallelic combinations. In this way they produced several thousand intragenic recombination events of which the majority could be accounted for by gene conversion. The analysis of these events revealed a general trend in conversion with a U-shape, suggesting that conversion initiates preferentially at either the 5' or 3' end of the bz gene but rarely extends to the entire length of the gene. Overall this study suggests that recombination initiation sites within genes are polarized in maize. Andrea Gallavotti, 2014.

10/2014 Candice Hirsch
Dyer, GA et al. 2014. Proc Natl Acad Sci, USA 111:14094-14099
   Genetic erosion in maize's center of origin

Crop genetic diversity is an essential resource for farmers and breeders responding to the changes in climate as well as pest and disease pressures that we are facing. Countless studies have demonstrated extensive genotypic and phenotypic diversity in maize, and much of this diversity has been captured and maintained in germplasm banks. However, unlike germplasm banks, in situ conservation allows crops to evolve in response to changing pests, diseases, and climate changes. On farm diversity in Mexico, the center of origin for maize, is an essential part of maintaining diversity that is continuously evolving in response to these changes. Average varietal richness per farm is a key statistic for in situ diversity conservation in crops. In this paper, the authors compare farm richness estimates based on cross-sectional case study data and longitudinal survey data from representative rural farms in Mexico to assess conservation. They show there has been significant decrease in maize diversity based on these metrics, and provide a social perspective to these changes. This is the first study to formally assess genetic erosion in a center of crop diversity and has significant implications surrounding conservation of maize diversity. Candice Hirsch, 2014.

10/2014 Andrea Gallavotti
Durbak, AR et al. 2014. Plant Cell 26:2978-2995
   Transport of boron by the tassel-less1 aquaporin is critical for vegetative and reproductive development in maize

As highlighted last month, the micronutrient boron (B) is essential for plant development. In this paper, Durbak et al. isolated and characterized the tassel-less1 (tls1) mutant of maize and showed that tls1 encodes a member of the aquaporin family of channel proteins. Transport assays in frog oocytes demonstrate that TLS1 facilitates the movement of boron across the membrane. In maize, tls1 mutants display boron transport deficiencies that result in reduced levels of cross-linked rhamnogalacturonan II (RG-II), a pectin polysaccharide that is a major structural component of the cell wall and requires boron to dimerize. These deficiencies at the cell wall cause widespread developmental defects, affecting meristem and organ development, and eventually maize fertility. The authors also show that crosses between tls1 and rte, a maize mutant caused by lesions in a specific boron efflux transporter (see September review), show environmentally dependent nonallelic noncomplementation, suggesting that the two proteins function in the same pathway to facilitate transport of boron from the root to the shoot of maize plants. The transport of boron via the concerted activities of channel and transporter proteins was previously shown in Arabidopsis, suggesting that this pathway is conserved between monocots and eudicots. While a basic pathway for boron uptake from the soil has been established, is still unclear how boron is distributed in the shoot and in inflorescences, despite its importance for worldwide crop productivity. The discovery of tls1 and rte and their role in inflorescence development and reproductive success provides the first tools to investigate this process in maize. Andrea Gallavotti 2014

10/2014 Madelaine Bartlett
Ding, Y, et al. 2014. BMC Plant Biology. 14:141
   Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana

In this study, the authors probe the intriguing phenomenon of "stress memory" in plants, where the first and subsequent biological responses to an abiotic stress are distinct. They compared the transcriptional response, using RNA-Seq, of maize seedlings after 1 and 3 dehydration stress-recovery events. Both maize and A. thaliana display a "memory response" to dehydration, but the character and dynamics of the response are divergent in these two species. For example, the regulation of the response appears to be divergent between the two species. Similar percentages of transcription factors were identified as "memory genes", but were enriched for very different functional classes. This study highlights the difficulty, in the study of complex phenotypic responses, of transferring information gained from one system to another over millions of years of evolution. Madelaine Bartlett, 2014

9/2014 Andrea Gallavotti
Chatterjee, M et al. 2014. Plant Cell 26:2962-2977
   The boron efflux transporter ROTTEN EAR is required for maize inflorescence development and fertility

In crops, proper boron nutrition is critical for obtaining high yields and high quality harvests. In maize, low levels of boron in the soil affect vegetative and in particular reproductive development, eventually causing widespread sterility in its inflorescences. This work reports the isolation and characterization of a novel maize mutant, rotten ear (rte) that shows impaired development of maize inflorescences. Positional cloning revealed that it encodes a boron efflux transporter responsible for transporting boron to the xylem. rte is co-orthologous to the Arabidopsis BOR1 gene, the first boron transporter identified in plants. RTE can rescue the developmental defects of bor1 mutants, indicating that the function of this class of transporters is conserved in monocot and eudicot species. The severity of the rte phenotype correlates with the availability of boron in the soil and can be rescued by boric acid treatments. Microscopic imaging shows that boron deficiency triggers widespread cell death in rte mutant inflorescences. In a companion paper by Durbak et al. 2014, the authors identified an additional player in maize boron uptake, the tassel-less1 gene. Together these two genes constitute a major boron transport pathway that is essential to maize inflorescence development. Check back next month for a review of this paper. Elucidating the mechanisms of boron transport and its roles in plant growth will enable the design of new strategies to alleviate deficiency or toxicity problems and increase crop production in several areas of the world. Andrea Gallavotti, 2014.

9/2014 Candice Hirsch
Burdo, BL, et al. 2014. Plant J. 0:doi: 10.1111/tpj.12623
   The Maize TFome - Development of a transcription factor open reading frame collection for functional genomics

Understanding the regulation of gene expression is essential in our efforts to understand plant growth and development and to be able to generate improved crop plants. Transcription factors play an essential role in regulating gene expression through the recognition of cis-regulatory elements. Determining the genes regulated by transcription factors is an intensive process that first begins with identification of the TFome. As with other omes, the TFome is defined as the collection of all (or a significant set) of the transcription factors for an organism. In this paper, the authors characterize the maize TFome and provide recombination-ready vectors consisting of 2,017 unique maize transcription factors and co-regulators. These clones provide a unique resource for functional genomics in maize. Candice Hirsch, 2014.

9/2014 Madelaine Bartlett
Zhang, J et al. 2014. J Exp Bot 65:5063-5076
   The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.)

Entrez Gene entry given (100193776) and GenBank accession (JN409349) align to la1 (lazy1)

Leaf angle is an important agronomic trait, with a complex genetic architecture. In this study, Zhang and colleagues worked to clone the gene responsible for a large leaf angle QTL, qLA4-1, responsible for 36.82% of leaf angle variance in a cross between D132 and Yu82. Fine mapping and positional cloning identified ZmLAZY1 (ZmLA1, referred to as ZmCLA4 in the manuscript) as a likely candidate gene underlying qLA4-1. The authors identified coding region SNPs between the two variants, a subset of which were associated with leaf angle variation in a panel of 75 inbred lines. qRT-PCR, RNAi lines in maize, and an overexpressor line in rice all provided evidence that higher expression levels of ZmLA1 are negatively correlated with leaf angle, and positively correlated with gravitropic response. There were also leaf-anatomical changes associated with ZmLA1 variation, but at this stage it is unclear how, exactly, this variation might impact leaf angle. All in all, this paper represents a step forward in characterizing the molecular infrastructure of phenotypic variability. Madelaine Bartlett, 2014.

8/2014 Matthew Hufford
Lemmon, ZH; Doebley, JF. 2014. Genetics 198:345-353
   Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL

There are currently no comments for this article.

8/2014 Madelaine Bartlett
Wu, C; Diggle, Pamela; Friedman, W. 2013. Proc Natl Acad Sci, USA. 110:2217-22
   Kin recognition within a seed and the effect of genetic relatedness of an endosperm to its compatriot embryo on maize seed development

The endosperm and the embryo in angiosperm seeds are both the products of a fertilization event, but the endosperm does not pass on its genetic material. Instead, the endosperm is consumed by the embryo and the developing seedling. This role for the endosperm in development might be considered in terms of the evolutionary theory surrounding altruism, genetic conflict, and cooperation. There has been much theorizing about these ideas as they relate to angiosperm reproduction, but few experimental studies. This paper presents one such study. The authors used maize as a system to test one key prediction arising from the theory: the degree of cooperation between an endosperm and its sister embryo should be correlated with genetic relatedness. Maize exhibits a phenomenon termed heterofertilization, where the egg and the central cell can be fertilized by sperm from two different pollen tubes. Using a combination of rare heterofertilization events, divergent inbred lines, and variation at the R color locus, the authors found evidence for conflict between the embryo and the endosperm in heterofertilized kernels. Although it remains uncertain as to whether or not there is a connection between this conflict and fitness, this study presents important empirical evidence for one piece of longstanding evolutionary theory. Madelaine Bartlett, 2014.

8/2014 Candice Hirsch
Jamann, TM et al. 2014. Genetics 198:333-344
   Unraveling genomic complexity at a quantitative disease resistance locus in maize

Extensive genome-wide structural variation has been demonstrated in maize including presence/absence variation, copy number variation, and structural rearrangements. However, there are a limited number of examples where structural variants have been linked to a phenotype. One notable example in maize is the MATE1 copy number variant that is associated with aluminum tolerance (Maron et al., PNAS 2013). In this paper, the authors dissected a quantitative disease resistance locus that can condition resistance to both northern leaf blight and Stewart's wilt. The region that the two overlapping QTL mapped to showed little to no recombination suggesting possible structural variation between the parents of the mapping population. Using read depth variation as an estimate of copy number variation, the authors found large variation in read depth across the region between Tx303 and the reference genome. This data further suggests that structural variation may be important in the disease resistance at the locus. Candice Hirsch, 2014.

8/2014 Andrea Gallavotti
Xiong, W et al. 2014. Proc Natl Acad Sci, USA 111:10263-10268
   HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

Helitrons are a rather mysterious class of transposable elements found in both plant and animal genomes. They were first identified by bioinformatics analysis in the late nineties. Helitrons comprise a unique class of transposable elements that lack terminal inverted repeats and target site duplications, are highly divergent, and whose mechanism of transposition is not yet fully understood. Nonetheless, they make up a significant amount of the DNA found in plant genomes. Helitrons have been shown to capture gene sequences and regulatory elements, and therefore have the potential to play an important role in genome evolution. In this paper, Xiong et al. developed a new tool for identifying Helitrons in plant genomes, called HelitronScanner. HelitronScanner identified more than thirty thousand new Helitrons in the maize B73 genome (6.6% of the genome) and identified Helitrons in plant species where no Helitrons had yet been reported. Compared to previously published tools, HelitronScanner is capable of detecting more divergent elements and provides a clearer representation of the Helitron content of different plant genomes. The increased number of Helitrons identified in this study helped to define a short but universal pattern shared by the majority of Helitrons that may help to shed light on the mechanism of transposition. Andrea Gallavotti 2014.

7/2014 Andrea Gallavotti
Li, Q; Eichten, SR; Hermanson, PJ; Springer, NM. 2014. Genetics. 196:667-676
   Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines

The regulation of gene expression by epigenetic modifications occurs in many eukaryotic organisms. DNA methylation is a major contributor to epigenetic regulation of gene expression and is established de novo by small RNAs and maintained by different methyltransferases. To better understand the frequency of epigenetic changes within a population over time as well as the inheritance of differentially methylated regions (DMRs) over multiple generations, in this study the authors analyze the inheritance of approximately 1000 DMRs from a panel of 71 near-isogenic lines (NILs) derived from B73 and Mo17 inbreds. The goal of this study was to characterize the inheritance and stability of these DMRs in the near-isogenic population. By characterizing methylation levels using an array-based approach they determined that i) in the majority of the loci, methylation level differences are stably and locally (cis) inherited across generations and do not require reprogramming by small RNAs and ii) only a few loci are influenced by other alleles or genomic regions due to paramutations or trans-acting control. Determining the stability and inheritance of epialleles in segregating as well as natural populations is crucial to our understanding of gene expression regulation, and its role in the rich phenotypic diversity observed in all species. Andrea Gallavotti 2014.

7/2014 Candice Hirsch
Li, L, et al. 2014. Genome Biol. 0:doi: 10.1186/gb-2014-15-2-r40
   Genome-wide discovery and characterization of maize long non-coding RNAs

The central dogma of "DNA makes RNA make protein" over simplifies the role of RNA in regulation of gene expression. In fact, numerous classes of non-coding RNA molecules have been defined, such as small nuclear RNAs, small nucleolar RNAs, microRNAs, small interfering RNAs, and long noncoding RNAs (lncRNAs) among others. The class of lncRNAs is defined as being greater than 200 bp in length and non-protein coding. Next generation sequencing technologies have allowed for genome-wide characterization of these lncRNAs in numerous animal and plant systems, and functional roles for lncRNAs are being discovered. In this paper, the authors surveyed all public EST and RNAseq datasets to comprehensively annotate putative lncRNAs in maize and classified them as likely small RNA precursors (18,459) and high confidence lncRNAs (1,704). Tissue specific expression was observed for 54% of the lncRNAs compared to 8% of the B73 filtered gene set based on the Shannon entropy measure of tissue-specificity. Interestingly, eQTL analysis revealed that maize lncRNAs are more affected by trans genetic factors than by cis genetic factors. This study provides a powerful tool for downstream research to characterize the functional roles of lncRNAs in maize. Candice Hirsch, 2014.

7/2014 Matthew Hufford
Schaefer, RJ; Briskine, Roman; Springer, NM; Myers, CL. 2014. PLoS One. 9:e99193
   Discovering functional modules across diverse maize transcriptomes using COB, the co-expression browser

Transcriptome-wide studies of correlation in gene expression across samples (i.e., co-expression studies) represent a powerful and increasingly popular approach for functional characterization of specific genes and identification of candidates relevant to a trait of interest. In their recent manuscript, Schaefer and co-authors build two co-expression networks using data generated from 1) 60 different tissues/stages of the maize reference line B73 and 2) 62 diverse maize and teosinte lines. Clusters of genes within these two networks were enriched for gene ontology categories, showing clear functional coherency. Gene clusters also contained many unannotated genes allowing for putative functional characterization based on "guilt by association". The co-expression networks developed in this project have been made publicly available in COB: The Co-expression Browser ( As illustrated in two case studies presented in the manuscript, COB represents a valuable new tool for functional characterization in maize. Matthew Hufford, 2014

7/2014 Nancy Salazar
Hughes, TE; Langdale, JA; Kelly, S. 2014. Genome Res. 0:
   The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole genome duplication in maize

There are currently no comments for this article.

7/2014 Madelaine Bartlett
Nestler, J et al. 2014. Plant J 79:729-740
   Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase

Root hairs, which represent up to 77% of the root surface of cereals, are instrumental in plant nutrient acquisition. The molecular genetics underlying the precise patterns of root hair initiation characteristic of Arabidopsis have been fairly well characterized. In maize, however, where root hair initiation is unpredictable, the process is far less understood. Up until now only a handful of genes controlling root hair initiation and growth have been cloned. In this paper, the authors report the cloning of one more gene: roothairless5 (rth5). rth5 was identified from an EMS mutagenesis screen and produces fewer, shorter root hairs. rth5 encodes an NADPH oxidase, and may produce the ROS that trigger cell wall loosening and growth of the root hairs. Exactly how rth5 might work, as well as upstream patterning mechanisms remain elusive, but this paper represents a step forward in understanding this agronomically important aspect of plant growth and development. Madelaine Bartlett, 2014

6/2014 Madelaine Bartlett
John, CR; Smith-Unna, RD; Woodfield, H; Covshoff, S; Hibberd, JM. 2014. Annu Rev Plant Physiol Plant Mol Biol. 165:62-75
   Evolutionary convergence of cell-specific gene expression in independent lineages of C4 grasses

The evolution of C4 photosynthesis requires drastic changes at both the anatomical and at the molecular level. The photosynthetic apparatus needs to be compartmentalized into mesophyll vs. bundle sheath cells. C4 photosynthesis has evolved at least 20 times in the grasses, and it is unclear whether the required molecular specialization and compartmentalization was achieved through similar or divergent mechanisms each time. To begin to answer this question, the authors conducted deep-sequencing (RNA-Seq) analyses of bundle sheath and mesophyll cells from Setaria viridis and compare their data to an existing Zea mays dataset. Setaria and Zea represent two separate derivations of C4 photosynthesis. Genes recruited into the C4 photosynthetic pathway showed a high degree of convergence in terms of expression in either the bundle sheath or the mesophyll, especially when compared to other genes not involved in photosynthesis. One intriguing result was that, although multiple paralogs were available in the ancestral genomes of Setaria and Zea, all 10 of the core C4 enzymes used by both species were syntenic orthologs. A similar result was also observed for key transcription factors. This implies that the same gene copies were repeatedly and independently recruited in each of the two lineages. It will be fascinating to see if this pattern extends beyond Setaria and Zea, to other more distantly related C4 lineages. Madelaine Bartlett, 2014

6/2014 Nancy Salazar
Yan, H et al. 2014. Biochem Biophys Res Commun 0
   Different evolutionary patterns among intronless genes in maize genome

There are currently no comments for this article.

6/2014 Matthew Hufford
Sharma, A; Presting, G. 2014. Genome Biology. 0:
   Evolution of centromeric retrotransposons in grasses

Centromeric retrotransposons (CRs) are a particularly interesting class of elements due to their ability to target functional centromeres as insertion sites, a phenomenon that may be due to the paucity of genes in centromeres or perhaps because of a potential role of CRs in centromere function. In their recent manuscript, Sharma and Presting conduct a comparative genomic analysis of CRs in maize, sorghum, rice, and foxtail millet. They characterize six different subfamilies of these elements and discuss evidence for horizontal transfer of CRs across the species boundary. Horizontal transfer is supported in multiple instances by very young divergence times in CRs that post-date speciation. Potential mechanisms proposed for horizontal transfer include viruses and rare instances of pollen flow between species. These mechanisms have been observed in the grasses (pollen flow) and other systems (viral horizontal gene transfer). Additionally, the authors find evidence for recombination both within and between subfamilies of CRs. Based on their analysis, the authors propose two compelling hypotheses: 1) Horizontal transfer and recombination in CRs may allow them to circumvent transposition control mechanisms of their previous hosts; and 2) Horizontally transferred CRs may be able to seed centromere formation in their new hosts. Matthew Hufford, June 2014

6/2014 Andrea Gallavotti
Li, G et al. 2014. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1406383111
   Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing

Endosperm is the reservoir of proteins and carbohydrates necessary for seedling growth, and in cereal crops such as maize, it provides an essential source of food worldwide. During the first few days after pollination the maize endosperm develops from a multinucleate cell into a cellularized structure, with different cell types and specialized functions: the starchy endosperm accumulates starch and proteins; the basal endosperm layer regulates nutrient transport from the maternal tissue; the aleurone produces enzymes that degrade the endosperm reserves upon germination; and the embryo surrounding region that supports embryo development. This specialized organization occurs thanks to highly regulated transcriptional and translational activities. In this paper transcriptomic analysis of the early stages of kernel and endosperm development is presented. Eight developmental time points are analyzed by RNAseq, providing a detailed picture of transcriptional activity. The onset of transcription factors (TF) expression is given particular attention. Coexpression analysis and clustering identified two groups of TF activity, one correlated to cell type differentiation, and another one correlated to the regulation of reserve accumulation in the endosperm. Validation of several of these genes by in situ hybridizations identified a series of genes with tissue specific expression patterns, including one expressed specifically in a newly identified cell type. This study provides a reliable and robust analysis of transcription in kernel and endosperm development, and together with the recently published proteome of developing seeds (Walley et al., PNAS 2013 ¿¿¿ Maize Editorial Board, February 2014), represents a significant step in deciphering the spatiotemporal programs that operate in cell differentiation and reserve accumulation during seed development. Andrea Gallavotti 2014.

6/2014 Candice Hirsch
Bi, YY, et al. 2014. BMC Genomics. 15:77
   High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation

Nitrogen is an important production input associated with high crop yields, but also with negative environmental effects and high economic costs. Additionally, corn plants do not incorporate the majority of the nitrogen that is applied in agricultural settings. Developing plants with improved nitrogen use efficiency will reduce environmental impacts and decrease production costs. In this paper, the authors used RNA-seq to evaluate the transcriptome of two inbred lines and their hybrid under nitrogen sufficient and limited conditions. The authors observed a large number of differentially expressed genes between the growth conditions within each genotypes and substantially more genes expressed under the nitrogen limiting condition. Comparisons between the three genotypes revealed different mechanisms to deal with nitrogen limiting growth conditions. However, gene expression in the hybrid more closely resembled the parental line with superior nitrogen use efficiency. This study adds to our understanding of nitrogen use efficiency, a trait with both environmental and economic importance. Candice Hirsch, 2014.

5/2014 Matthew Hufford
Lang, Z et al. 2014. J Hered 105:576-582
   Defining the Role of prolamin-box binding factor1 Gene During Maize Domestication

Multiple lines of evidence have previously suggested that the prolamin-box binding factor1 (pbf1) gene was targeted by selection during the domestication of maize. This gene encodes a transcription factor that is known to control expression levels of seed storage proteins (zeins). Since maize kernels are substantially larger than teosinte kernels, pbf1 is a compelling candidate for further characterization. In their recent study, Lang and co-authors assessed kernel phenotypes, pbf1 expression, and zein protein profiles in near-isogenic lines (NILs) with both maize and teosinte alleles at the pbf1 locus. Surprisingly, the authors found two-fold higher expression and larger and heavier kernels in plants with the teosinte allele rather than the maize allele. The authors also could not detect expression-level differences in known targets of pbf1 and no differences in zein profiles could be attributed to the presence of a teosinte versus maize allele. A number of potential confounding factors and explanations for these largely negative results were mentioned including environmental effects and the influence of a mostly maize background in the NILs on domestication differences due to pbf1. The authors concluded by cautioning that the identification of phenotypes altered by domestication can be quite challenging, even when the candidate under consideration has a well-known biological function. Matthew Hufford, 2014

5/2014 Madelaine Bartlett
Kim, H, Kim, JS, 2014. Nat Rev Genet 15:321-34
   A guide to genome engineering with programmable nucleases

Targeted genome editing using programmable nucleases has great potential as a tool for geneticists of all flavors. There are three main types of programmable nucleases that might be of utility in probing gene function: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and RNA-guided engineered nucleases (RGENs). RGENs, in particular, have been the subject of much discussion in the plant community recently, as part of the CRISPR/Cas9 system (Clustered Regular Interspaced Short Palindromic Repeat/CRISPR-associated protein 9). Although not focused on their use in plants, this paper offers a timely review of all three systems: how they work, and each of their pros and cons. Madelaine Bartlett, 2014.

5/2014 Nancy Salazar
Luan, M et al. 2014. PLoS One 9:e91369
   Family-wide survey of miR169s and NF-YAs and their expression profiles response to abiotic stress in maize roots

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5/2014 Candice Hirsch
Martin, JA et al. 2014. Scientific Reports 4: DOI: 10.1038/srep04519
   A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

Next generation sequencing has expanded the breadth and depth of questions that biologist are now able to ask. Next generation sequencing has already been used to study the genome, transcriptome, and epigenome of maize and other species. However, as with any technology, it is important to understand both the benefits and limitations of next generation sequencing approaches. In this paper, the authors address an important question relating to consequences of sequencing depth with regards to RNA sequencing (RNA-seq) using extremely deep sequencing of the B73 seedling transcriptome. Among the findings in this paper, the authors show that relative to simulated ???shallow sequencing??? (20 million reads), they were able to detected on average 7,444 more 5b transcripts, and showed that many of the missed transcripts were associated with transcription factor activities. They were also able to improve the current B73 structural annotation including expanding gene models and identifying unannotated genes. This manuscript provides important insights on sequence depth considerations, which in part depends on the scientific goals of that study. Candice Hirsch, 2014.

5/2014 Andrea Gallavotti
Rice, EA; et al. 2014. PLoS One. 9:e94238
   Expression of a Truncated ATHB17 Protein in Maize Increases Ear Weight at Silking

The dynamic regulation of transcription is essential for every aspect of plant growth. This is generally accomplished by both transcriptional activation and repression mechanisms. Recent evidence suggests that transcriptional repression is a common and widespread regulatory mechanism employed by many developmental and hormonal pathways. The homeodomain leucine zipper II (HD-Zip II) family of transcription factors is a large family whose members are known to homo and heterodimerize and to regulate an array of pathways. The Arabidopsis ATHB17 protein carries a well-known repressor motif (EAR motif) that confers transcriptional repression ability when tested in a protoplast-based repression assay. In this study the full-length HD-Zip II gene ATHB17 gene was overexpressed in maize, but it was soon noted that a truncated version of the protein lacking the EAR motif was produced. Since this truncated version retained the ability to homo and heterodimerize as well as bind DNA, it prompted the authors to investigate if it could act as a dominant negative to endogenous maize HD-Zip II proteins. By using the protoplast repression assay the authors showed that by adding increasing concentration of the truncated ATHB17 expression construct they were capable of decreasing the repressor ability of maize HD-Zip II proteins. Finally, the authors analyzed the phenotype of maize transgenic lines expressing the dominant negative version of the Arabidopsis ATHB17 and discovered an increase in ear weight without concurrent increase in vegetative biomass in replicated field plots. Analysis of the transcriptome of these lines revealed only subtle changes in global transcript levels in ears. Overall, these results show the importance of studying the mechanisms of transcriptional regulation in plants, a knowledge that can provide new molecular tools to improve crop performance by modulating transcription. Andrea Gallavotti, 2014.

4/2014 Nancy Salazar
Zhang, H et al. 2014. J Integr Plant Biol 56:262-70
   Meta-analysis and candidate gene mining of low-phosphorus tolerance in maize

Breeding crop cultivars that could uptake and use soil phosphorus (P) more efficiently is critical for alleviating phosphate waste and increasing resource use efficiency in agriculture. Understanding of genetic mechanisms of low-P tolerance can help to develop low-P tolerant cultivars. The authors are focused to discover information that is important for genetics and molecular breeding of low-P tolerance in maize through meta-analysis and candidate gene mining using all QTL and molecular information currently available. Meta-analysis is an important tool for integration information from multiple quantitative trait loci (QTLs) studies from independent genetic mapping activities, which allows greater statistical power for QTL detection and more precise estimation of their genetic effects. The consensus QTL (cQTL) identified by QTL meta-analysis could delimit the QTL confidence interval and decrease the number of candidate genes. The authors identified 23 cQTL, representing 131 original QTLs using Biomercator 2.1 software and IBM2 2008 Neighbors map as the reference map, all the QTL from original maps were projected onto this map, forming QTL clusters. Among the cQTLs, 9 containing 22 genes, which are homologous to 14 genes collected from Arabidopsis, rice and white lupin. The homologs of the 22 genes in the cQTL regions are OsMYB2P-1, AtPht1;1, LaGPX-PDE2, OsPSTOL1, AtMYB2, AtLPR1, AtPHO1, miR399h, miR399i, AtSUC2, AtPht2;1, AtMGD2, AtWRKY75, AtPAH1 and AtPAP10; which were functionally characterized to influence plant low-P tolerance, and could be candidates of gene mining with possible roles in maize low-P tolerance. This study has narrowed each of 19 cQTL to less than a 10Mb interval and 4 cQTL to less than 1 Mb, that can be used for candidate locus association mapping. Miriam Salazar, 2014.

4/2014 Andrea Gallavotti
Sutimantanapi, D et al. 2014. Plant Physiol 164:1905-1917
   Divergent roles for maize PAN1 and PAN2 receptor-like proteins in cytokinesis and cell morphogenesis

Leucine-rich receptor-like proteins belong to a large gene family in plants and are used in many developmental pathways to activate downstream signaling cascades. Whereas the majority of these proteins have an active kinase domain (leucine-rich receptor-like kinases or LRR-RLKs), others lack kinase activity and are thought to function via interaction with active kinases. The maize PAN1 and PAN2 proteins belong to the latter category of LRR-like proteins and were originally identified for their function in guiding asymmetric cell divisions during stomata development. It was previously reported that PAN1 functions with Type I ROP GTPases, well known to regulate actin polymerization, and that PAN2 functions upstream of PAN1 in regulating cell polarity. In this report the authors investigate whether PAN1 and PAN2 play additional roles in other cellular processes since their expression is observed in different tissue types with actively dividing cells. This work shows that PAN1 and PAN2 have indeed additional distinct roles in cells. In particular, PAN2 is involved in regulating cell shape by affecting the accumulation of actin in a manner that is independent of PAN1 and Type I ROP GTPases, and PAN1 on the other hand participates in the development of the cell plate, the new cell wall that separates daughter cells, and acts independently of PAN2 in this process. Although the mechanisms remain to be elucidated, the authors propose that PAN proteins function either directly or indirectly via actin polymerization in all cellular contexts. Andrea Gallavotti, 2014.

4/2014 Madelaine Bartlett
O'Connor, D, et al. 2014. PLoS Comput Biol. 10:e1003447
   A division in PIN-mediated auxin patterning during organ initiation in grasses

Auxin is a key player in plant morphogenesis: the hormone has been implicated in almost every aspect of patterning. For example, directional auxin transport is known to play an important role in patterning plant vasculature and organ positioning. Competing models have arisen, all trying to explain how the auxin efflux transporter PIN-FORMED1 (PIN1) of Arabidopsis thaliana works to concentrate auxin into maxima necessary for organ initiation, and also create the narrow auxin flows necessary for vein formation. This new paper adds to the debate by investigating the PIN1-like proteins in Brachypodium distachyon. The authors identified three PIN1-like genes in B. distachyon: PIN1a, PIN1b, and Sister-of-PIN1 (SoPIN1). PIN1a and PIN1b appear to be the products of a grass-specific gene duplication. Intriguingly, SoPIN1 was found in all sampled angiosperms except for Brassicaceae family members. SoPIN1 seems to have been lost somewhere along the lineage leading to Arabidopsis and the broader Brassicaceae. Fluorescent protein fusion lines were used to follow auxin (by DR5 proxy) and the expression of all three transporters in developing B. distachyon inflorescences. The protein and auxin localization patterns suggest clear distinctions between the three proteins¿¿¿ roles: SoPIN1 creates an auxin maximum, PIN1b directs developing veins to older auxin sinks, and PIN1a refines auxin flow to a narrow vascular stream. Immunolocalization experiments suggest a similar mechanism in maize. Although there are no functional data in the grasses to support the authors¿¿¿ hypotheses, a computational model they developed reproduces their experimental observations. The results reported in this paper offer a compelling argument for investigating both auxin and PIN dynamics in a range of angiosperm taxa. Madelaine Bartlett, 2014

4/2014 Matthew Hufford
Gassmann, AJ; et al. 2014. Proc Natl Acad Sci, USA. :
   Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize

Over the past few decades, the cultivation of transgenic maize producing insecticides derived from Bacillus thuringiensis (Bt) has become a widespread pest-management strategy in the American Corn Belt. This strategy has proven successful in managing western corn rootworm, a major pest of maize. In their recent manuscript, Gassmann and co-authors describe the development of resistance of western corn rootworm in Iowa to two similar Bt toxins expressed in transgenic maize, Cry3Bb1 and mCry3A. Resistant populations were found in an increasing number of fields during the period from 2009-2011 suggesting either spread of resistant individuals or multiple instances of resistance evolving. Cross-resistance was also documented, i.e., rootworms were resistant to both Bt toxins. Resistance arose rapidly over a period of less than four years of exposure to these Bt toxins, a phenomenon attributed to the low dose of these toxins expressed in maize lines. While the authors confirmed that another Bt toxin (Cry34/35Ab1) is still effective in controlling western corn rootworm, this study begs caution in managing pest resistance to transgenic crops. Refuge strategies and additional integrated pest management will likely prove essential in delaying pest resistance. Matthew Hufford, 2014.

4/2014 Candice Hirsch
Lamkey, CM; Lorenz, AJ. 2014. Crop Sci. 54:576-585
   Relative Effect of Drift and Selection in Diverging Populations within a Reciprocal Recurrent Selection Program

Maize hybrid breeding benefits greatly from heterotic pools that generate superior hybrids when inbred lines from opposite heterotic pools are crossed. The initial formation of heterotic pools in North American germplasm is a fascinating story (see Tracy and Chandler, Plant Breeding: The Arnel R. Hallauer International Symposium, 2006). Overtime, genetic divergence has occurred between the heterotic groups. Likewise, recurrent selection programs show similar genetic divergence overtime. However, it is not clear if this divergence is the result of section or random genetic drift. At the University of Nebraska, a replicated recurrent selection program was performed that allowed the authors of this study to address the question of the role of selection and drift in the establishment of strong heterotic patterns. Results of this study demonstrate the importance of genetic drift for population differentiation during reciprocal recurrent selection and possibly in shaping population structure of North American maize. Candice Hirsch, 2014

3/2014 Nancy Salazar
Bolduc, N; Tyers, RG; Freeling, M; Hake, S. 2014. Plant Physiol. 164:229-238
   Unequal redundancy in maize knotted1 homeobox genes

Class I knox transcription factors represent a gene family expressed in meristems and excluded from leaves. In this work the authors elucidated in maize, the role of the class I Knox gene rough sheath1 (rs1), which is only revealed in the complete absence of Knotted1 (kn1), the founding member of knox gene family. When kn1 is missing, absence of rs1 has an impact in shoot phenotype showing a limited shoots and reduced tassel branch number; otherwise kn1 will compensate for the loss of rs1 function. In contrast, rs1 cannot substitute for kn1 in kn1 mutant. In rice, similar unequal redundancy is observed between kn1 and osh1 homeobox genes in the maintenance of the shoot apical meristem. Here, the authors conclude that the knox hierarchy is conserved between rice and maize, in the orthologous pairs kn1-osh1 and kn1-rs1. In addition, the authors show that while KN1 and RS1 are both necessary for shoot development in the inbred lines B73 and Mo17, rs1;kn1 double mutants recover when not fully introgressed into B73, suggesting the possible action of modifier loci highlighting the possibility of another players in meristem maintenance. Miriam Salazar, 2014.

3/2014 Matthew Hufford
Piperno, DR; Holst, I; Winter, K; McMillan, O. 2014. Quaternary International. 0:ePub ahead of print
   Teosinte before domestication: Experimental study of growth and phenotypic variability in Late Pleistocene and early Holocene environments

Domestication of several crops around the world, including maize, occurred approximately 10,000-12,000 years ago. Environmental conditions at this time differed dramatically from current conditions; for example, carbon dioxide, temperature, and precipitation levels were all considerably lower in the New World tropics where maize was domesticated. In their recent manuscript, Dolores Piperno and co-authors report their investigation of phenotypic plasticity in the wild ancestor of maize (Zea mays ssp. parviglumis; hereafter, parviglumis) grown in chambers under current environmental conditions and those approximating the time of domestication (low carbon dioxide and temperature). Multiple parviglumis plants grown under domestication conditions were characterized by maize-like phenotypes, having few lateral branches tipped with female inflorescences, whereas all parviglumis plants in current conditions were more typical of wild Zea with multiple lateral branches tipped with tassels. The authors also observed a marked reduction in productivity of parviglumis grown in conditions during the timeframe of domestication. The remarkable, environmentally mediated phenotypic plasticity observed here suggests parviglumis encountered by early foragers and cultivators may have more closely resembled modern maize. Questions remain as to whether early cultivators' selection on these plastic responses could have led to a genetic underpinning and canalization of domestication traits. Matthew Hufford, 2014.

3/2014 Madelaine Bartlett
Tanaka, S et al. 2014. Elife 3:e01355
   A secreted Ustilago maydis effector promotes virulence by targeting anthocyanin biosynthesis in maize

Interactions between plants and their pathogens are mediated in part by effector proteins produced by the pathogen. Ustilago maydis (corn smut) is a biotrophic fungal pathogen of maize. U. maydis infection causes both the development of tumors and anthocyanin accumulation in infected tissues. U. maydis produces hundreds of effector proteins, the function of most of which remains unknown. In this paper, the authors elucidate the function of one U. maydis effector, Tin2. The authors show that Tin2 is a secreted protein that stabilizes a maize protein kinase, ZmTTK1, by binding to a ubiquitin-proteosome degradation motif in ZmTTK1. The stabilization of ZmTTK1 results in increased anthocyanin biosynthesis, possibly because of phosphorylation of the transcription factor R1, allowing R1 to enter the nucleus and upregulate anthocyanin biosynthesis. The authors devise an interesting model where this upregulation of anthocyanin biosynthesis diverts metabolic precursors from the lignin biosynthetic pathway. Reduced lignin biosynthesis may result in plant cells more susceptible to fungal infection, thus increasing pathogen virulence. This model is supported by analyses of U. maydis pathogenicity in biosynthetic mutants of maize. U. maydis pathogenicity was attenuated when the biosynthetic pathway to anthocyanins was blocked in chalcone synthase (c2) mutants. Lignin-affected brown midrib (bm) mutants showed U. maydis hypersensitivity. Anthocyanin accumulation is not unique to the U. maydis-maize pathogen/plant interaction. The authors may have uncovered a host metabolic rewiring strategy common to a number of plant pathogens. Madelaine Bartlett, 2014.

3/2014 Andrea Gallavotti
Lituiev, DS et al. 2013. Annual Review of Cell and Developmental Biology 140:4544-53
   Theoretical and experimental evidence indicates that there is no detectable auxin gradient in the angiosperm female gametophyte

The female gametophyte of most flowering plants is composed of four types of cells: synergid, egg, central and antipodal cells. It was previously proposed that fate specification of these cells is determined by an auxin gradient oriented along the micropylar to chalazal axis inside the female gametophyte that behaves in a morphogen-like manner. The formation of auxin gradients has recently been implicated in many developmental processes. In this report the authors employ mathematical models to explain the formation of the proposed auxin gradient in the female gametophyte, but determined that only shallow gradients could be achieved. In their models the authors took into account various parameters such as auxin efflux and influx, localized auxin biosynthesis and degradation, as well as the presence of the large vacuole that forms inside the female gametophyte. The theoretical gradients achieved in all conditions were determined to be too shallow to withstand small perturbations inherent to biological systems and therefore unlikely to provide the robust positional information for cell fate specification in the female gametophyte. By using in vivo imaging of fluorescent reporters for auxin response in both maize and Arabidopsis ovules, the authors show that auxin responses are not detected in the female gametophyte but rather in the surrounding sporophytic tissue. Based on these results they propose that the effect of auxin in providing positional information for cell fate specification in the female gametophyte of flowering plant is likely indirect. Andrea Gallavotti, 2014.

3/2014 Candice Hirsch
Hirsch, CN et al. 2014. Plant Cell 26:121-135
   Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in all individuals (core) or only in a subset of individuals (dispensable). Collectively the core and dispensable genome comprise the species pan-genome. In bacteria, it is thought that dispensable genes contribute to diversity and adaptation, and much of the early work to characterize species level pan-genomes was conducted in bacteria. More recently, pan-genome studies have been conducted at various levels in plant and animal systems. In this paper, we used transcriptome sequencing as a proxy for genome sequences to explore the maize pan genome across 503 diverse maize inbred lines. We identified nearly 9,000 novel representative transcript assemblies. Additionally, using linkage disequilibrium mapping and syntenic analysis were able to place nearly a third of these novel transcripts on the B73 genome assembly. Using SNP and expression variants in the maize pan genome, genome-wide association studies revealed loci associated with the timing of the juvenile to adult vegetative and vegetative to reproductive developmental transitions, two traits important for fitness and adaptation. This manuscript greatly expands on our understanding of the dynamic nature of the maize pan genome and the contribution of various levels of diversity to adaptive traits. Candice Hirsch, 2014

2/2014 Madelaine Bartlett
Waters, AJ. et al. 2013. Proc Natl Acad Sci, USA 110:19639-19644
   Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species

Imprinting, the differential expression of maternally- and paternally-derived alleles, was initially described in maize, but has also been described (and studied) in mammals. Imprinting is particularly interesting to students of epigenetic reprogramming, and those considering theories of genetic conflict. In plants, the endosperm is the main site of imprinting. Until the advent of next-generation sequencing techniques like deep sequencing of RNA (RNA-Seq), only a handful of imprinted genes had been identified. This new paper represents a comprehensive analysis of imprinting in maize, across four divergent maize genotypes. The experimental design allowed the identification of both maternally and paternally expressed genes (MEGs and PEGs), as well as genes that showed allelic variation for imprinting. One observation the authors make is that MEGs and PEGs are usually treated as a single class, but their analyses reveal a few distinctions. For example, MEGs are far more likely to be endosperm-specific in their expression, while PEGs are more often associated with H3K27me3. In line with previous investigations, very little overlap in imprinted genes was discovered both between maize genotypes, and between maize and rice. Those genes that were identified as conserved within and between species, however, represent an interesting set of targets to pursue in studies of gene function. Madelaine Bartlett, 2014.

2/2014 Candice Hirsch
Walley, JW, et al. 2013. Proc Natl Acad Sci, USA. 110:E4808-17
   Reconstruction of protein networks from an atlas of maize seed proteotypes

Genome-wide atlases of gene expression have been generated in many plant species, including maize (see Sekhon et al, The Plant Journal, 2011). These large datasets can provide valuable insights into expression patterns among tissues and organs as well as expression throughout the course of development, and are extremely useful in addressing an array of biological questions. Often, measures of transcript abundance are used to infer the proteome of a cell, tissue, or organ. However, in this paper, the authors took on the major task of generating a quantitative atlas of proteotypes from different seed components throughout development using mass spectrometry. Interestingly, the authors also demonstrated poor correlation between mRNA levels and protein abundance. Because of the quantitative nature of the data, the authors were able to reconstruct biochemical and signaling networks important for seed development and the production of seed storage products and provide valuable new insights into seed development. Candice Hirsch, 2014.

2/2014 Nancy Salazar
Bolduc, N; Tyers, RG; Freeling, M; Hake, S. 2014. Plant Physiol. 164:229-238
   Unequal redundancy in maize knotted1 homeobox genes

Class I knox transcription factors represent a gene family expressed in meristems and excluded from leaves. In this work the authors elucidated in maize, the role of the class I Knox gene rough sheath1 (rs1), which is only revealed in the complete absence of Knotted1 (kn1), the founding member of knox gene family. When kn1 is missing, absence of rs1 has an impact in shoot phenotype showing a limited shoots and reduced tassel branch number; otherwise kn1 will compensate for the loss of rs1 function. In contrast, rs1 cannot substitute for kn1 in kn1 mutant. In rice, similar unequal redundancy is observed between kn1 and osh1 homeobox genes in the maintenance of the shoot apical meristem. Here, the authors conclude that the knox hierarchy is conserved between rice and maize, in the orthologous pairs kn1-osh1 and kn1-rs1. In addition, the authors show that while KN1 and RS1 are both necessary for shoot development in the inbred lines B73 and Mo17, rs1;kn1 double mutants recover when not fully introgressed into B73, suggesting the possible action of modifier loci highlighting the possibility of another players in meristem maintenance. Miriam Salazar, 2014.

2/2014 Matthew Hufford
Mezmouk, S; Ross-Ibarra, J. 2014. G3 4:163-171
   The pattern and distribution of deleterious mutations in maize

Most newly arising mutations are thought to be deleterious and should be kept at low frequency, particularly when their negative effects on fitness are strong. Despite their rarity, deleterious mutations are believed to play an important role in disease and variation in quantitative traits and may, through the process of complementation, underlie hybrid vigor observed in crosses between heterotic groups of maize. In their recent study, Mezmouk and Ross-Ibarra conduct a genome-wide analysis of putatively deleterious mutations across a panel of 247 maize inbred lines. Using prediction software to gauge the effects of amino acid changes, the authors estimate that 20-40% of coding SNPs have a deleterious allele segregating in their sample. Based on analysis of phenotypic data from their panel, the authors find that genes containing deleterious mutations are more likely to be associated with hybrid vigor. This latter result provides compelling evidence consistent with the dominance hypothesis of heterosis; deleterious mutations in one heterotic group may be complemented by an alternative allele in another. In addition, while previous work has suggested elevated residual heterozygosity in pericentromeres may be caused by inefficient selection in these regions due to their low recombination rate, Mezmouk and Ross-Ibarra find no enrichment of deleterious mutations in pericentromeres suggesting there is enough recombination over the long-term for their removal through selection. Matthew Hufford, 2014.

2/2014 Andrea Gallavotti
Eveland, AL, et al. 2013. Genome Res. 0:DOI: 10.1101/gr.166397.113
   Regulatory modules controlling maize inflorescence architecture

Meristem activity shapes the architecture of plant inflorescences and is responsible for the vast diversity of reproductive structures found in nature. Meristems can have a determinate or indeterminate fate. In the former case they terminate in a differentiated structure, such as a flower, whereas in the latter case they prolong their activity and form branches. In maize, the ramosa mutants (ramosa1, ramosa2, ramosa3) are all characterized by a loss of meristem determinacy and as a result ears and tassels show various degrees of branching. In this report, Eveland et al. employed the ramosa mutants as tools in a series of genomic approaches aimed at understanding the regulation of meristem determinacy. Using a combination of RNA-seq analysis of all three mutants and ChIP-seq of the zing-finger transcription factor RAMOSA1, this report identifies genome-wide targets of RA1 activity, defines its binding sites and provides evidence for both positive and negative regulation of downstream transcriptional targets. Interactions with previously known factors regulating inflorescence architecture, such as liguleless1 and knotted1, are described. Overall, this report provides detailed expression profiling of the early stages of ear and tassel development and identifies regulatory networks involved in meristem activity. Andrea Gallavotti, 2014.

1/2014 Nancy Salazar
Garsmeur, O, et al. 2013. Mol Biol Evol. 0:doi: 10.1093/molbev/mst230
   Two evolutionarily distinct classes of paleopolyploidy

It has been described previously that two sub-genomes can be identified in maize, the result of an ancestral whole genome duplication (WGD) event. The two sub-genomes differ in dominance and exhibit biased fractionation (the process of gene loss following WGD), which suggests questions about the retention of duplicated gene pairs. In this paper, the authors propose a generalized fractionation-dominance model, where bias in gene expression is responsible for bias in gene loss within the genome. Based on sub-genome behaviour, the authors recognize two classes of WGD event: Class I, in which one sub-genome shows a higher level of gene expression than the other, and an associated greater rate of gene retention; Class II, in which sub-genomes show equal gene expression, associated with unbiased fractionation. The authors propose that Class I is associated with ancient allotetraploidies, while Class II is associated with ancient autotetraploidies. Their analysis of gene deletion and gene expression in maize, positions it within Class I. Miriam Salazar, 2014

1/2014 Madelaine Bartlett
Moon, J et al. 2013. Plant J 76:592-602
   Regulation of cell divisions and differentiation by MALE STERILITY32 is required for anther development in maize

Maize anthers, and indeed those of all angiosperms, contain a series of clearly defined cell types and cell layers. This paper provides new insight into the genetic regulation of the development of these cell layers. The male sterile 32 (ms32) mutant exhibits extra cell layers, that fail to differentiate as expected (the tapetum fails to differentiate). Pollen mother cells are squashed by the extra somatic cell layers and fail to go through meiotic prophase one, resulting in male sterile plants. ms32 encodes a bHLH transcription factor expressed specifically in pre-meiotic anthers. ms32 is the ortholog of the rice gene UNDEVELOPED TAPETUM1 (UDT1), but the mutant phenotypes in rice and maize are distinct (although background effects were not investigated). Apart from identifying one more genetic player in the development of anthers, this study presents an interesting example of divergent functions of orthologous genes in fairly closely related species, in a process one would think would be highly conserved in flowering plants as a whole. Madelaine Bartlett 2014.

1/2014 Matthew Hufford
Wang, K et al. 2013. Genome Res pp.doi:10.1101/gr.160887.113
   Maize centromeres expand and adopt a uniform size in the genetic background of oat

While centromeres, as assembly sites for kinetochores responsible for chromosomal segregation, serve an essential function, their position along a chromosome is somewhat labile. In this investigation, Wang and co-authors characterize centromere lability in nine oat-maize addition lines in which a single maize chromosome has been introduced into an oat background. Previous work had shown that total centromere area is correlated with genome size. The genome of oat is roughly four times the size of maize with oat having only twice the number of chromosomes. The authors therefore hypothesize that maize centromeres in oat-maize addition lines should double in size. Using chromatin immunoprecipitation for the centromeric histone CenH3, the authors measure maize centromere size in addition lines and find their hypothesis to be well supported; while the average maize centromere in its native context is 1.8 Mb, the centromeres of maize chromosomes in oat-maize addition lines is closer to 3.6 Mb, stretching into gene-poor regions. Moreover, two addition lines containing maize chromosome 3 show formation of neocentromeres in which the original position of the maize centromere has changed entirely. In both cases, neocentromeres form in gene-poor regions with the majority of genes in these regions not being expressed. The findings of Wang and co-authors importantly suggest that, despite lability in centromere position, constraints of genome size and gene density determine the area occupied by centromeres. Matthew Hufford, 2014

1/2014 Andrea Gallavotti
Bommert, P et al. 2013. Nature 502:555-558
   The maize Gα gene COMPACT PLANT2 functions in CLAVATA signalling to control shoot meristem size

Meristems are small group of stem cells responsible for post-embryonic plant development. Throughout development meristems need to constantly create new organs at their flanks as well as maintain their core stem cell niche to avoid termination. In some species, meristems are maintained for decades. A well-established pathway for meristem maintenance is the WUSCHEL-CLAVATA (WUS/CLV) negative feedback loop, first identified in Arabidopsis based on analysis of mutants defective in shoot apical meristem maintenance. In maize, a similar pathway exists and members of this pathway have been isolated throughout the years by studying mutants with fasciated inflorescences. This new report by Bommert et al. identifies a previously undiscovered player in this pathway, COMPACT PLANT2 (CT2) that encodes the G-alpha subunit of a heterotrimeric GTP binding protein. Heterotrimeric G proteins are well-known secondary messengers that link signals emanating from seven-pass transmembrane G-protein coupled receptors to various intracellular effectors. In this paper, CT2 is shown to genetically and physically interact with the LRR-receptor like protein FEA2/CLV2, suggesting that CT2 is part of the signaling pathway that controls meristem size and challenging the common belief based on studies in yeast and animal systems that G-alpha proteins only interact with seven-pass transmembrane G-protein coupled receptors. This discovery may explain how LRR-receptor like proteins, such as FEA2/CLV2 that lack a kinase domain, can transmit an intracellular downstream signal. Finally, this report represents another nice example of the importance of using different model systems to dissect complex developmental pathways. Andrea Gallavotti, 2014.

1/2014 Candice Hirsch
Romay, MC et al. 2013. Genome Biology 14:R55
   Comprehensive genotyping of the USA national maize inbred seed bank

Characterizing genetic diversity and the genetic architecture of phenotypic traits is important for addressing issues related to sustainable agriculture and climate change. The body of literature on the role of rare allelic variants in phenotypic diversity is growing rapidly. Identifying rare variants through GWAS is difficult and requires large sample sizes. GWAS studies in maize to date have used relatively small diversity panels, and as such do not represent the breadth of rare variants in maize. In this paper, the authors genotyped the entire USA national maize inbred seed bank, which contains 2,815 inbred accessions from breeding programs all over the world. Of the nearly 700K identified single nucleotide polymorphisms (SNPs), nearly half were rare in the collection. Additionally, the data set showed that, while much of the available diversity has been incorporated into public temperate breeding programs, only a modest amount is present in commercial germplasm. The utility of this data set for performing genome-wide association studies (GWAS) was tested. While associations were identified for SNPs near candidate genes, the authors suggest that even higher SNP density may be needed to fully characterize the genetic architecture of complex quantitative traits. Candice Hirsch, 2014.

12/2013 Amanda Wright
Dong, Z, et al. 2013. Plant Physiol. 163:1306-1322
   Maize LAZY1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling and light response

In this paper, Dong et al. report the phenotypic characterization and cloning of the maize ZmLA1 gene. This thorough analysis places ZmLA1 at the intersection of gravitropism, inflorescence development, light and auxin signaling. A classic maize mutant, la1 plants have a prostrate stem phenotype and the shoot fails to exhibit a robust gravitropic response. In addition, tassel and ear development are abnormal. In other plants, disruption of ZmLa1 homologues results in less severe gravitropic defects while the inflorescences develop normally. In maize, ZmLa1 is expressed in ears and tassels as well as the nodes of the stem and expression increases in the dark. In onion cells, ZmLA1-GFP localizes to the nucleus and plasma membrane. Basipetal polar auxin transport is enhanced in the ears, tassels, and coleoptiles of the mutants while lateral polar auxin transport is decreased in the la1 coleoptiles suggesting that ZmLA1 normally acts to inhibit basipetal polar auxin transport and enhance lateral auxin transport. A yeast two-hybrid screen identified 8 interacting proteins including two known to be involved in auxin signaling. RNA-SEQ experiments identified 646 up-regulated genes versus 285 down-regulated genes in la1 plants compared to wild type suggesting that ZmLA1 also functions as a transcriptional repressor. Some of the differentially expressed genes are involved in auxin response or transport. Amanda Wright 2013

12/2013 Ruairidh Sawers
Lu, Y et al. 2014. Plant Reproduction 27:19-20
   Genetic and cellular analysis of cross-incompatibility in Zea mays

In Mexico, the ancestral home of maize, there is great interest in gene flow among populations of ancestral teosinte, landrace maize, and imported hybrid varieties. Here, Lu and colleagues remind us that, in addition to ecological factors and cultural practice, plant biology plays a key role also in this process. Three genetic systems have been well described that confer cross-incompatibility between domesticated maize and wild teosinte. While the molecular mechanisms underlying these systems remain elusive, Lu and colleagues provide further data that extend our knowledge of the genetic basis of the Teosinte crossing barrier1 (Tcb1) locus. Cross-incompatibility barriers consist of two functions, female and male: the female function confers the silk-barrier to incompatible pollen; the male function determines the competence of pollen to fertilize silks expressing the female function. While a rare haplotype that confers male function only has been identified in natural teosinte populations, Lu and colleagues, through detailed analysis of recombinants, separate genetically the female and male functions of a Tcb1, suggesting a possible complex locus. Further, the authors characterize arrest of pollen-tube growth in incompatible interactions. Intriguingly, the morphology of arrested pollen-tubes is different between Tcb1 and other known cross-incompatibility systems, suggesting that various mechanisms may be involved. Finally, the authors report the loss of cross-incompatibility in lineages carrying active Mutator transposons. The potential availability of transposon-tagged alleles of Tbc1 has clear implications to the molecular identification of the gene or genes that constitute the Tbc1 locus. As the authors point out, cloning of the genes involved will go a long way to finally untangling the history and mechanism of one of the great stories of maize population biology. Ruairidh Sawers, 2013

12/2013 Thomas Slewinski
Meihls, LN et al. 2013. Plant Cell 25:2341-2355
   Natural Variation in Maize Aphid Resistance Is Associated with 2,4-Dihydroxy-7-Methoxy-1,4-Benzoxazin-3-One Glucoside Methyltransferase Activity

In this paper, Meihls and colleagues report the identification and cloning of the first aphid susceptibility QTL in maize. Using the natural variation present in the NAM population, the authors were able to detect a large effect, almost mendelian, aphid susceptibility QTL on Chromosome 1. Susceptibility was associated with the absence of a DOPIA transposon insertion into one of three tandem nearly identical O-methytransferase genes, Bx10a, b and c. The insertion into Bx10c was further associated with higher levels of DIMBOA-Glu, a benzoxazinoid defense compound that is known to induce callose formation in the plant and is toxic to aphids, thus resulting in plants that are more resistant. Susceptible lines that have a functional copy of Bx10c gene convert more DIMBOA-Glu to HDIMBOA-Glu, which is more toxic to aphids, but does not induce callose deposition, and presumably other subsequent defense responses, as strongly as DIMBOA-Glu. This study highlights the trade-offs between the defense-inducing properties and direct toxicity to insects conferred by the variants of maize benzoxazinoids. Thomas Slewinski 2013

12/2013 Lewis Lukens
McCarty, DR, et al. 2013. PLoS One. 8:e77172
   Mu-seq: Sequence-based mapping and identification of transposon induced mutations

Insertional mutagenesis with the Robertson's Mutator transposon has been important for both forward and reverse genetics in maize. The availability of a large collection of lines with insertions within many different genes is a key resource for gene function investigations. Families within the Uniform-MU population contain novel and stable Mu transposon insertions. There are currently over 45,500 germinal Mu insertions in over 8,236 maize lines. In this report, McCarty et al. describe a novel method for identifying Mu insertions within Uniform-MU families using targeted high-throughput sequencing. They start by assigning each of 576 families a position on a 24 x 24 grid. They extract two DNA samples on the opposite sides of plants from the 576 families. One DNA sample is pooled with a set of 23 families along a grid row, and the other DNA sample is pooled with a set of 23 families along the column. An analysis of Mu insertions within the 24 row and 24 column samples can identify the precise family in which an insertion has occurred by using the intersection of the two axes in which an insertion is detected. A problem with this approach is that Mu elements are numerous within the maize genome, and it can be tricky to identify novel insertions among ancestral insertions. Here, McCarty et al. selectively amplify flanking sequence from only the terminal inverted repeats of Mutator transposons that are most active in plants with autonomous MuDR elements. With about 100 million 100 bp sequence reads, McCarty et al.'s method identifies 4,723 novel, germinal transposon insertions- insertions detected both in one column sample and in one row sample. The method distinguishes distinct Mu insertions at the same locus when the insertion sites differ by as little as a single nucleotide. Interestingly, 13,218 insertions have substantial sequence support but were found in a single column or row sample, suggesting somatic insertions of Mu. These single axis reads are greatly over-represented in certain samples suggesting that about 1% of the families have Mu activity. Mu activity remains despite selection against activity based on bz1-mum9 expression, perhaps because of epigenetic phenomena. Lewis Lukens 2013

11/2013 Lewis Lukens
Regulski, M et al. 2013. Genome Res 23:1651-62
   The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

Cytosine methylation is an epigenetic modification of DNA that can affect gene expression and occurs in three sequence contexts: CG, CHG (where H is A, C, or T), and CHH. In this work, Regulski et al. present a genome-wide map of cytosine methylation from maize inbreds B73 and MO17 in all three contexts by deep sequencing sodium bisulfite treated DNA. (Sodium bisulfite converts unmethylated cytosines to thymines.) They compared methylation patterns with sRNA and mRNA abundances as well as with DNA attributes. As expected, they found evidence of dense methylation in the pericentromeric regions of each chromosome, strong correlation between 24nt sRNA levels and CHH methylation, and low levels of cytosine methylation in exonic DNA relative to 5' and 3' DNA. A number of discoveries were especially interesting. They identify a spike of cytosine methylation at splice junctions. Acceptor sites with a high level of CHG methylation were less efficiently spliced than acceptor sites with low methylation levels, and among those genes that are alternatively spliced and have acceptor sites with different levels of methylation, the large majority of genes used the acceptor site with the reduced CHG methylation. They also identify highly differentially methylated regions between B73 and MO17. Methylation differences are correlated with expression levels of nearby genes, suggesting that these differences may contribute to trait differences between the two inbred lines. Most of the parental methylation patterns were found to be inherited along with parental alleles across nine recombinant inbred lines derived from the two parents, but about 0.9 Mb of the 6 MB of differentially methylated regions switched methylation states. A higher frequency of regions became hypermethylated than hypomethylated; hypermethylation occurs at a higher frequency within MO17 alleles than B73 alleles; and the same regions switch epigenetic states more than expected by chance. The mechanism that directs these epigenetic inheritance patterns is still unknown. Overall, Regulski et al suggests a fascinating possibility- that paramutation-like methylation changes lead to significant changes in gene regulation at an unexpectedly high frequency. Lewis Lukins 2013

11/2013 Amanda Wright
Liu, S et al. 2013. PLoS Genetics 9:e1003790
   Genome-Wide Analysis of ZmDREB Genes and Their Association with Natural Variation in Drought Tolerance at Seedling Stage of Zea mays L

Previous studies in maize and Arabidopsis reported that the DREB family of transcription factors are important for responding to various abiotic stresses including drought. Lui et al. (2013) identified 18 DREB genes in the maize genome and showed that they are all up-regulated in seedlings grown under drought conditions. Taking advantage of the natural variation between maize lines, the authors used recently published SNP data to determine that 14 of the 18 DREB genes are polymorphic within a diversity panel containing 368 lines. They also evaluated all 368 lines for drought stress tolerance. After compiling the SNP information and drought phenotypes, an association analysis determined that polymorphisms in one gene, ZMDREB2.7, correlated strongly with drought resistance. Supporting this finding, transforming Arabidopsis with ZmDREB2.7 resulted in drought resistance plants. Additionally, after crossing drought sensitive and drought resistant lines, segregation of sensitive/resistant alleles in the F2 population correlated with the drought resistance phenotype of the plants. This gene can now be targeted in breeding efforts to generate more drought-tolerant plants. Amanda Wright 2013

10/2013 Amanda Wright
Derrer, C, et al. 2013. Plant Cell. 25:3010-3020
   Conformational changes represent the rate-limiting step in the transport cycle of maize SUCROSE TRANSPORTER1

SUT1 is a symporter that allows the accumulation of high concentrations of sucrose in phloem cells by coupling the unfavorable transport of sucrose with the favorable transport of protons across cell membranes. Building on previous work investigating the molecular mechanisms of ion-coupled transporters in E. coli, animals, and plants, Derrer et al. propose a model for the early stages of SUT1 mediated transport. The authors identified sucralose, the artificial sweetener commercially sold as Splenda, as a competitive inhibitor of SUT1. When sucralose is bound to SUT1, SUT1 can still bind protons, but the transport of the protons across the membrane is inhibited. They used voltage clamp fluorometry (VCF), a technique that detects conformational changes in a protein, to determine that sucrose transport is coupled to the movement of an extracellular loop and sucralose inhibits this conformational change. VCF works by fusing a flourophore to an accessible amino acid with subsequent changes in fluorescence intensity indicative of movement of the fluorophore and thus a conformational change of the protein. Their final model is that SUT1 continuously changes conformation so that the binding site is alternative exposed the interior and exterior of the cell. Upon proton binding, the current conformation is stabilized allowing for binding of the sugar. Overall, this study provides a fascinating view into the intricate workings of a transporter critical for the movement of sugars from source to sink tissues in plants. Amanda Wright 2013

10/2013 Lewis Lukens
Rodriguez, VM, et al. 2013. J Exp Bot. 64:3657-3667
   Genetic regulation of cold-induced albinism in the maize inbred line A661

As the geographical range of maize expands, it is increasingly subject to low temperatures both early and late in the growing period. Thus, there is great interest in uncovering natural variation for cold tolerance and the genes that contribute to it. Seedling leaves of the inbred line A661 have a dramatic reduction of chlorophyll content when the plant is exposed to a chilling temperature below 15C. This work revealed that the chlorophyll reduction was unlikely due to chlorophyll degradation in A661 nor due to a non-functional chlorophyll biosynthesis pathway. The authors suggest that at cool temperatures, A619 chlorophyll is not stably integrated into photosynthetic antennae, remains free in the chloroplast, and activates the expression of an early light inducible protein gene that prevents reactive oxygen species accumulation. The cold induced albinism is likely caused by a number of alleles. The strongest QTL on chromosome 2 explains a 14% of the phenotypic variation. The identity of this gene and other contributing genetic factors will be of significant interest. Lewis Lukens, 2013

10/2013 James Schnable
Maddonni, GA; Otegui, M; Andrieu, B; Chelle, M; Casal, J. 2002. Plant Physiol. 130:1181-1189
   Maize leaves turn away from neighbors

Seeds planted using a hand planter end up planted in the ground with a random orientation, yet when walking through a field planted at high densities, I'll often noticed that the leaves of most plants tend to be orientated perpendicularly to the path of the row and very few plants are orientated so that their leaves press directly against neighboring plants in the same row. A canopy made of leaves orientated perpendicular to rows instead of parallel captures more of the total sunlight falling on the field while decreasing competition between neighboring plants. In this paper the authors show that maize plants from one hybrid background actively reorient their leaves away from simulated shade produced by altering the ratios of red to far red light falling upon the leaf (a signal perceived by the phytochrome light signaling pathway). A second hybrid line tested showed no change in leaf orientation in response to simulated shade. A better understanding of the pathways that allow maize plants to orient their leaves for maximum productivity and the level of variation that exists in current elite germplasm may prove to be important as commercial planting densities continue to increase. James Schnable, 2013

10/2013 Ruairidh Sawers
Zhang, J; Zuo, Tao; Peterson, TA. 2013. PLoS Genetics. 9:e1003691
   Generation of tandem direct duplications by reversed-ends transposition of maize Ac elements

Comparative analyses using chip hybridization and genome re-sequencing have revealed a great number of copy number variants (CNVs) present among maize lines and varieties. While clearly widespread, many questions remain unanswered regarding CNVs, both in maize and other organisms. Notably, how are they formed, and what is their functional significance? Zhang et al. address the former question, with a specific focus on tandem duplication. It has been hypothesized previously that tandem repeats are typically formed by non-allelic homologous recombination. Here, the authors suggest a further mechanism based on alternative transposition events catalysed by the termini of adjacent transposons. Through an elegant use of the kernel marker P1, the authors select and characterize molecularly a number of novel reciprocal deletion/duplication events. The authors go on to identify three further duplications in the B73 reference genome that bear all the hallmarks of formation following alternative transposition. Given the frequency of events uncovered in the study, alternative transposition may represent a specialized yet active modulator of genome size. Ruairidh Sawers, 2013

9/2013 Lewis Lukens
Eichten, SR, et al. 2013. Plant Cell. 25:2783-2797
   Epigenetic and genetic influences on DNA methylation variation in maize populations

In this study, Eichten et al. profile DNA methylation levels across a set of maize genotypes by enriching for methylated DNA fragments and hybridizing the fragments to a microarray containing 2.1 million probes surveying the low-copy portion of the maize genome. They make a number of interesting discoveries, including the following. First, the DNA methylation levels of many chromosomal regions differ. They identify 1966 regions where at least three of the 19 lines have DNA methylation patterns that differ from other lines. 1754 regions have discrete methylation patterns in one or two lines only. The rare variants tend to be hypomethylated relative to the common variants. Second, Eichten et al. find that most of the differentially methylated regions are heritable, and for many regions, the methylation state is cis regulated. Many differentially methylated regions are associated with nearby transposons. Finally, Eichten et al. suggest a functional importance for differentially methylated regions because DNA methylation levels at a number of regions correlate with transcript abundance at nearby genes. High levels of methylation within regions that overlap genes' transcription start sites are negatively correlated with transcript abundances. Naturally occurring chromatin differences likely explain a proportion of the genetic variation within plant populations. This is especially true in maize because its genome has a high number of transposable elements, and many genes are located close to transposons. This work offers a fascinating snapshot of DNA methylation variation and offers a number of areas for further inquiry. Lewis Lukens, 2013

9/2013 Ruairidh Sawers
Venkata, BP, et al. 2013. PLoS One. 8:e71296
   crw1- A novel maize mutant highly susceptible to foliar damage by the western corn rootworm beetle

The corn rootworm complex (Diabrotica sp.) presents one of the greatest current pest challenges to maize cultivation: traditional pest-management strategies based on crop rotation are being rendered less effective by insect behavioural change; rootworm-protected transgenic varieties are not universally accessible, and there are concerns regarding resistance development. Despite the evident importance of the so-called "billion dollar bug", much remains to be learnt about the biology of the interaction. Venkata and colleagues provide striking new evidence regarding the choice of food-source by adult corn rootworm beetles. While, as the name suggest, corn rootworm larvae feed primarily on roots, adults feed on pollen and silks, as well as on neighbouring non-maize vegetation. Leaves, however, are typically untouched by either juveniles or adults. Here, the authors report a novel mutant (crw1) that exhibits a severe susceptibility to foliar damage by the adult beetles. When pest numbers are high, the effect is dramatic: the leaf blades of adult plants can be completely stripped. The author's observations demonstrate clearly that what appeared to be a passive interaction is anything but. In the wild-type plant the nature of the leaf surface in some way deters the beetles from feeding, while the beetles themselves are actively making a choice of food-source - a choice that they are happy to change when they encounter crw1 mutant plants. Targeting the adult beetles is an attractive strategy to incorporate into any corn rootworm management program. A greater understanding of the interaction between plant and pest has great potential to inform such efforts. Ruairidh Sawers, 2013.

9/2013 Amanda Wright
Facette, MR; Shen, Zhouxin; Bjornsdottir, Fjola ; Briggs, S; Smith, LG. 2013. Plant Cell. 25:2798-812
   Parallel proteomic and phosphoproteomic analyses of successive stages of maize leaf development

Facette at el. presents a comprehensive proteomics survey of the developing maize leaf. Using mass spectrophotometry, they identified ~12,000 proteins and ~3,500 phosphoprotiens within 4 developmentally distinct leaf zones including the cell division zone, cell differentiation zone, cell expansion zone, and mature blade tissue. Careful examination of the proteins revealed that while many proteins are found in all four zones, there is also a large number of proteins expressed in the division, differentiation, and expansion zones and excluded from the mature leaf blade. While the differentiation, division, and expansion zone have a similar complement of proteins, the identified phosphoproteins were more likely to have a zone specific distribution. Highlighting the usefulness of this data set for hypothesis generation, the authors took a close look at cell wall synthesis proteins as well as the proteins involved plant hormone production and response. They were able to identify expected as well as unexpected trends in protein and phosphoprotein distribution. Overall, the proteomic data discussed in this paper is a valuable community resource that complements existing mRNA expression data. Amanda Wright, 2013

8/2013 Thomas Slewinski
Wills, D et al. 2013. PLoS Genetics 9:e1003604
   From many, one: Genetic control of prolificacy during maize domestication

There are many common morphological shifts that take plant during plant domestication. One of the most prominent alterations, especially in grain crops, is the reduction in number and increase in size of the inflorescence - known as prolificacy. Wills et al. explore the underlying genetic basis of this trait in maize using a genome-wide QTL scan of teosinte-maize recombinant inbred lines to identify causative regions responsible for the shift from 100 or more small ears in teosinte, to one or two large ears in maize. The authors show this trait has a relatively simple genetic architecture that can mostly be attributed to one large-effect QTL located on the short arm of chromosome 1. The causative genomic region maps to the promoter of the grassy tillers1 (gt1), a transcription factor that functions in axillary bud outgrowth suppression. The maize prol1.1 region causes a gain of expression and function of gt1 in the nodal plexus of the meristem which leads a reduction in ear-forming axillary branches-conditioning the domesticated trait. Importantly, this study highlights how simple and subtle changes in gene expression can cause dramatic shifts in the productivity and harvestability in plants. Tom Slewinski 2013

8/2013 Amanda Wright
Zhang, YF; Hou, MM; Tan, BC. 2013. PLoS One. 8:e67369
   The requirement of WHIRLY1 for embryogenesis is dependent on genetic background in maize

In this paper, Zhang et al. report the cloning of the emb16 mutant and the discovery that emb16 is allelic to a previously cloned mutant, why1. why1 encodes a RNA/DNA binding protein needed for genome stability and ribosome assembly in plastids. emb16 in the W22 background is embryo lethal while why1-1 in a different genetic background results in albino seedlings. Extensive molecular analysis of expression and protein levels suggest that emb16 and why1-1 are both null mutations, however, the emb16/why1-1 complementation tests produce in a mixture of embryonic lethality and albino seedling phenotypes. These findings indicate that differences in genetic backgrounds can result in alternate phenotypes when the WHY1 protein is missing. Mutants lacking two other proteins needed for plastid protein synthesis also show background dependent phenotypes suggesting that some genetic backgrounds either do not require robust plasmid protein synthesis for embryogenesis or have unknown compensatory mechanisms. There is no apparent paralogue of WHY1 in any genetic background removing the simpler explanation that a hidden paralogue is compensating for the loss of WHY1. Additionally, while originally reported to localize to chloroplast, this paper reports that WHY1 also localizes to the nucleus. This paper serves as a reminder about the complexities of the maize genome and its evolutionary past and the impact it can have on mutant analysis. Amanda Wright 2013

***'emb12' locus described here is apparently different from that descibed by Clark & Sheridan (see: Locus is now called emb17.

8/2013 James Schnable
Thurber, CS et al. 2013. Genome Biology 14:R68
   Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production

Sorghum is crop species that is a close relative of maize and, like maize, was originally domesticated in the tropics but now widely grown in temperate environments. These similar life stories mean than much of the genetic diversity of both species is found in tropical environments that do grow well (or at all) in temperate environments like the American midwest. This paper takes advantage of a research program that has been increasing the genetic diversity available to temperate sorghum breeders by crossing NILs of diverse tropical sorghum landraces using a temperate adapted line as the donor parent and selecting for temperate adaptation in each round of backcrossing. The authors compared 580 "exotic progenitor" lines to temperate adapted lines derived from each progenitor using genotyping-by-sequencing. They identify fixed introgressions across all the temperate adapted NILs of known temperate adaptation loci including loci that regulate flowing time and dwarfism. Intriguingly they also identify regions of the genome where donor parent sequences have become fixed only within NILs derived from specific subpopulations of tropical germplasm. Overall this paper is another demonstration of how cheap genotyping is allowing biologists to study the genetic causes behind the variation breeders are selecting for. James Schnable, 2013

8/2013 Lewis Lukens
Zhai, J et al. 2013. Plant Cell 25:2417-2428
   Plant microRNAs display differential 3' truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species

Small RNAs are key regulators of many plant processes. For example, most plant miRNAs are bound by ARGONAUTE1 (AGO1), a key component of the RNA Induced Silencing Complex (RISC), that uses miRNA as templates to specify mRNA targets. The Arabidopsis HUA ENCHANCER1 (HEN1) encodes a methyltransferase that methylates the 3' end of sRNAs, including miRNAs. In hen1 mutant backgrounds, the abundance of microRNAs (miRNAs) is reduced, and unmethylated miRNAs undergo 3' modifications including truncation and oligo-uridylation (tailing) that is associated with their degradation. In this work, Zhai et al. deeply sequence sRNAs from wild type and hen1 mutants from Arabidopsis, maize, and rice. They find that in hen1 mutants, 3' ends of miRNAs have a diversity of truncated and tailed forms. Interestingly, the patterns of truncation and tailing differ across miRNA families but are broadly conserved across species- points that are nicely illustrated with graphical representations of counts of miRNAs with different truncation and tailed attributes. They also discover that AGO1 can bind truncated and tailed miRNAs, and an ago1 mutation suppresses the 3' modifications of miRNAs in hen1. This finding indicates that the 3' miRNA modifications occur when miRNAs are in association with AGO1. Although the 3' truncation and tailing of miRNAs is relatively infrequent, the authors observe some similar patterns in wild type plants, and the work fundamentally contributes to an understanding of miRNA function and regulation. Lewis Lukins, 2013

8/2013 Ruairidh Sawers
Pei, L et al. 2013. Plant Physiol Biochem 70:221-234
   Identification and comparative analysis of low phosphate tolerance-associated microRNAs in two maize genotypes

MicroRNAs (miRNAs) are one of a number of species of small non-coding RNAs implicated in fine-tuning the regulation of development, nutrient homeostasis and the response to abiotic stress. The role of the miRNA system in governing plant responses to changes in internal phosphate status has been intensively studied in the model plant Arabidopsis. Indeed, the systemic action of the miRNA mir399 during phosphate starvation provides one of the best understood examples on a plant miRNA acting in a stress response. Here, the authors use Solexa sequencing to analyse small RNA libraries prepared from the roots of control and phosphate-starved maize seedlings, generating a catalogue of phosphate-starvation regulated miRNAs that included both members of previously described families and novel sequences. The authors include also in their analysis phosphate-starvation tolerant and intolerant lines. While it is difficult to identify causal variants directly from such a comparison of two varieties, it is intriguing to note that the authors do observe a number of miRNAs that accumulate differentially between tolerant and intolerant lines. The authors conclude by pointing out the potential of targeting miRNAs in efforts to manipulate plants for greater stress tolerance. Given their mode of action-binding to a complementary target sequence-it is interesting to consider also the relative ease with which miRNA targets can be acquired and lost on the basis of single nucleotide changes. Ruairidh Sawers, 2013

7/2013 Ruairidh Sawers
Vigeland, MD et al. 2013. New Phytol 199:1060-1068
   Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

Local adaptation is a potent driver of diversity. The grass family (Poaceae), consisting of ~10,000 species, first evolved ~70mya in a warm climate, but has since dispersed and adapted, such that today grasses are found from tropical forests to freezing Arctic and Antarctic ecosystems. Among the present day grasses, the Pooideae sub-family (a species rich group, including many important crop species) has been particularly successful in adaptation to cold climates. Here, Vigeland and colleagues investigate both the timing and the mechanism of adaptive evolution to low-temperature in the grasses using a phylogenomics approach. The authors make use of the complete genomes of maize, sorghum, rice and Brachypodium, and partial sequence of wheat, barley, Lolium and Festuca. After determining orthology relationships among gene models identified from the various species, they produce a phylogenetic tree for each group of orthologs. Subsequently, they identify those trees that contain "low-temperature" genes, as defined a priori on the basis of transcriptomic analyses. Examining low-temperature trees to determine rates of molecular evolution, and for evidence of positive selection, the authors conclude that adaptation to cold-stress occurred early in the evolution of the Pooideae, and, as such, may have played a key role in expanding the niche-range and in the development of many of our most important crops. Ruairidh Sawers, 2013

7/2013 Thomas Slewinski
Kuntz, M et al. 2013. Nature Biotechnology 31:498-500
   What the French ban of Bt MON810 maize means for science-based risk assessment

Publications can have significant impacts political decisions regarding regulations and implementation of technology as well as choices of the general public in their selection of products and services. The recent controversy raised by a group claiming that transgenic maize and the associated herbicide both cause identical pathogenesis in mice (see Seralini et al. 2012. Food and Chemical Toxicology) has shaken the public's acceptance of scientific method and objective research. Kuntz et al. 2013 discuss the broad-sweeping impacts that this one report has had on both the public understanding of science and the national policies that conceived and enforced based on subjective interpretation of science. Surprising and truly unsettling trends are emerging in the public realm of science perception, not only in the fields of plant science and GM technology, but also in climate and health science (i.e. vaccination). However, such controversies also open up many opportunities for scientists to reach out and educate the the general public to increase the understanding and acceptance of science facts while reducing science fears which are gaining more and more prominence in many societies. Thomas Slewinski 2013

7/2013 Lewis Lukens
Strigens, A, et al. 2013. Plant Cell Environ. 36:1871-1887
   Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments

Chilling and cold temperature sensitivity limit the cultivation of maize in the Northern and Southern hemispheres, and breeding for chilling and cold tolerant varieties would increase yields in these areas. Here, Strigens et al. investigate physiological and developmental traits in a large set of inbred lines from North American dent, European dent, and European flint germplasm collections. They assay plants in several field locations and in a controlled environment with a mild chilling stress. To identify alleles that explain genotypic variation, they associate SNPs with genotypes' trait values. Estimates of genotypic variance are significant for all traits measured in field and chamber. For most chamber traits, genetic variation is significantly higher in plants grown in ~14C than in plants grown in the control temperature, ~25C. Flints are considered more cold tolerant than dents, but growth of dents is not unusually affected by the chilling temperatures. Genotypic values for biomass related traits measured in the chamber are moderately correlated with field growth rates. The inbred lines have high linkage disequilibrium, and Strigens et al. find a number of SNPs associated with photosynthesis and developmental traits. Many QTL correspond to candidate genes. One difficulty with genetic analyses of quantitative traits such as chilling tolerance is G x E. A genotype's performance in a chamber may not correlate well with the field, and a genotype's performance across different field trials may not correlate. This article discusses a number of interesting methods for data analysis. One nice example is the principle components analysis of extensive climactic information gathered from the multiple field sites. Components capture key environmental differences among the locations, and the authors correlate the allelic effects of QTL in each environment with the components from the PCA. Thus, they identify alleles that may be expressed in certain types of environments. Lewis Lukens 2013

7/2013 Amanda Wright
Guo, Xiaomei et al. 2013. Plant Physiol 162:1359-1369
   Non-redundant function of zeins and their correct stoichiometric ratio drive protein body formation in maize endosperm

Zein proteins, which are storage proteins organized into protein bodies, make up a majority of the protein expressed in the maize endosperm. Zein proteins have a poor amino acid profile, which limits the ability of maize endosperm to serve as a quality protein source. In order to manipulate zein protein content to improve grain quality, it is important to have a complete understanding of zein protein function and how the zeins are organized into protein bodies. Many of the zein protein families contain multiple members so Guo et al. (2013) used RNAi to knock down complete families in order to ascertain their function. In combination with previously published reports including a complementary zein RNAi study reported by Wu and Messing (2010), Guo et al. proposes specific roles for zein proteins in protein body formation. They suggest that although the gamma zeins co-localize to the outer layer of the protein body, the 27kD gamma zein is needed for protein body initiation while the other gamma zeins are needed for protein body expansion. Additionally, simultaneous depletion of the two alpha zein classes results in smaller protein bodies pointing to a role in expansion for the alpha zein classes. Interestingly, when the RNAi constructs targeting all the zeins are combined, the resulting endosperm contains small numbers of normally shaped and sized protein bodies suggesting that fixed zein protein ratios are also critical for protein body morphology and expansion. Amanda Wright 2013

6/2013 Lewis Lukens
Labonne, JDJ; Dorweiler, JE; McGinnis, K. 2013. Epigenetics. 8:398-408
   Changes in nucleosome position at transcriptional start sites of specific genes in Zea mays mediator of paramutation1 mutants

Chromatin and DNA modifications play key roles in transcriptional regulation and are associated with changes in nucleosome positioning. The maize gene Mediator of Paramutation1 (Mop1) is a homologue of an RNA dependent RNA polymerase (RDR2) that is required for the biogenesis of small RNAs that direct heterochromatin formation. Many maize genes are mis-expressed in the mop1-1 mutant. Here, Labonne et al. compare nucleosome positions between a mop1-1 mutant and a wild type control at the transcriptional start sites (TSSs) of about 400 maize genes in leaf, ear shoot, tassel, and seedling samples by hybridization of nucleosomal DNA to a high density microarray. In a subset of the tissues, three of the 400 genes had consistent differences in nucleosome positioning between mutant and wild type plants. Nucleosome positions differed both upstream and downstream of the TSSs. For two genes, positioned nucleosomes appeared to have been lost in the mutant plants, and for the third gene, a positioned nucleosome appeared to have been gained. Surprisingly, the nucleosome differences were not associated with differences in transcript abundance. This work suggests that MOP1 affects chromatin structure at a small proportion of maize gene TSSs, and that these modifications have an indirect, if any effect, on gene expression. The widespread transcriptional changes in mop1-1 seem not to be associated with TSS nucleosome distribution and are perhaps due to MOP1 mediated silencing of repetitive DNA. Lewis Lukens, 2013

6/2013 Thomas Slewinski
Arber, A. 1918. Ann Bot 32:465-502
   The phyllode theory of the monocotyledonous leaf, with special reference to anatomical evidence

There is a long-standing debate to whether monocots actually have true leaf blades. In 1918, Agnes Arber (available at outlined the phyllode theory of monocot evolution that hypothesizes that the ancestor to the monocots may have evolved in an aquatic environment. Adaption to an "aquatic habitat" lead to a reduction or loss of the leaf lamina (blade) and an extrapolation of the petiole and lower leaf into a new blade-like structure. Presumably this is why monocots have parallel venation in the leaves, because the reticulated vein pattering was lost with the true leaf blade, leaving only the parallel tracks of transport veins at the leaf base . In 1973, Donald Kaplan (available at further modified this theory by arguing that the extrapolated monocot leaf blade is derived from the "lower leaf zone" that is comprised of the "base" and the stipules found in dicot leaves instead of the upper region of the petioles as argued by Arber. The idea has dramatic implications on how monocots, especially the grasses, develop and function. This could also help to explain why there is such a dramatic divergence in structure and physiology in the grasses, such as maize, when compared to dicots, such as Arabidopsis. Thomas Slewinski, 2013

6/2013 Ruairidh Sawers
Burton, AL; Brown, KM; Lynch, JP. 2013. Crop Sci. 53:1042-1055
   Phenotypic Diversity of Root Anatomical and Architectural Traits in Zea Species

The domestication of cultivated maize from wild teosinte has become a text-book example of how far, and how fast, morphology can change in response to intensive selective pressure. Indeed, the extent of the difference between maize and teosinte is such that it was considered for a long time inconceivable that the two were any more than distant relatives. The story of maize domestication, however, has always been that of change to the aerial portions of the plant. What of the root system? Can so much be happening above ground without impacting the plant's "hidden half"? Here, Burton and colleagues provide perhaps the first detailed survey of the diversity to be found in maize and teosinte root systems. The authors characterize a panel of 256 accessions, including landrace and teosinte diversity, measuring a range of anatomical (e.g. area of cortex, steele, aerenchyma) and architectural (e.g. root number, root length) traits after 28 days of greenhouse growth. Intriguingly, the authors find significant differences between teosinte and landrace groups for a number of traits. It interesting to speculate on the impact of domestication on the root system, and the role root system adaptation may have had to play on the dispersal of maize. With respect to roots, there is clearly no "big bang" moment analogous to the formation of the cob: perhaps, a better analogy would be with the tassel (male inflorescence). Regardless, Burton and colleagues provide evidence that both landraces and teosintes represent an important source of root phenotypic variation, a source that may have much practical utility in future maize improvement. Ruairidh Sawers, 2013

6/2013 Amanda Wright
Li, JF et al. 2013. Plant Cell 25:1507-1522
   Comprehensive Protein-Based Artificial MicroRNA Screens for Effective Gene Silencing in Plants

Plant genome sequencing has uncovered thousands of uncharacterized genes creating the challenging task of assigning functions to all the proteins encoded by these genes. Using reverse genetics to create organisms that lack the unknown protein is one way to assign function. While the various collections of maize mutant lines available to the community continue to expand, there is not always a mutant available or functional redundancy with a paralogue complicates the analysis of the gene of interest. Gene silencing methods that exploit endogenous RNA degradation or translational repression pathways such as RNAi, VIGS, and amiRNAs provide an alternative way to knock down protein levels, but it is not unusual for a silencing construct to fail to work effectively. This can be especially problematic for species such as maize where generating transgenic plants is costly and time consuming. Li et al. (2013) describe a prescreening method to evaluate the efficiency of amiRNAs (artificial micro RNAs) designed in silico. They co-expressed an amiRNA along with an epitope-tagged full-length version of the target in Arabidopsis protoplasts. They then looked for loss of the epitope-tagged protein via Western. They screened multiple amiRNAs (usually four) that target the same gene identifiying the most effective amiRNA. In their test cases, they found that the amiRNAi that was the most effective at knocking down protein levels in protoplasts was also the most effective in plants. In addition to prescreening amiRNAs for knocking out an single protein, this technique can be used to test how effective a single amiRNA is at targeting multiple parologues or to test the effectiveness of multiple amiRNAs arranged polycitronically or tandemly. Based on their experience with the amiRNAi screens, the authors also provide some new rules for more effective amiRNA design. While much of the validation of this technique was carried out in Arabidopsis, the authors demonstrate that prescreening amiRNAs in protoplasts works in a wide variety of plants including maize. Amanda Wright, 2013

6/2013 James Schnable
Hufford, MB, et al. 2013. PLoS Genetics. 9:e1003477
   The genomic signature of crop-wild introgression in maize

Maize is now known to have been originally domesticated from a subspecies of teosinte called parviglumis which grows natively in the lowlands of central mexico. However much of the modern range of maize cultivation is in environments very different from the native habitat of parviglumis. In the article the authors report on extensive gene flow from another teosinte subspecies (mexicana) which grows alongside maize in the mexican highlands, measured using microarray based genotyping of SNP markers. Despite limited viability of crosses between mexicana and domesticated maize, the authors found that gene flow occurs in both directions. However, adaptive introgressions have occurred almost exclusively from the wild teosinte subspecies into domesticated maize. This result is consistent with a model where these introgressed regions are involved in adaption to colder and drier climate of the mexican highlands. Two putatively adapted introgressed loci are potentially involved in the differences in macrohair development between lowland and highland teosintes. James Schnable, 2013

5/2013 Amanda Wright
Jiang, WK et al. 2013. Plant Physiol 161:1844-1861
   Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants

As maize geneticists, we are often confronted with the maize genome's evolutionary past when we discover our favorite gene has a paralogue. These paralogous gene pairs often arise due to the whole genome duplication (WGD) events that are consistent features of the evolutionary past of many organisms, including the flowering plants. After a WGD genomes undergo fractionation, which includes genome rearrangements and gene loss. Previous studies have determined that duplicated genes can be retained and undergo neofunctionalization where one gene acquires a new fate or subfunctionalization where the duplicated genes split the function previously covered by the original gene. The study by Jiang et al. examined duplicated gene pairs found within areas of synteny in 6 plant genomes (maize, sorghum, rice, soybean, poplar, and Arabidopsis) and looked to see if they could identify features that made both members of a duplicated gene pair more likely to be retained. They evaluated 18 features and were able to divide the retained genes into three groups based on shared features. Type I genes evolve slowly, are highly expressed, and are involved in processes essential to cell survival suggesting their retention could be due to dosage compensation where having equal amounts of the proteins within a functional network is beneficial. Type II genes are structurally complex with many protein domains suggesting they are candidates for subfunctionalization. Type III genes are united by their high GC and GC3 (G/C present at the third codon position) content, fast evolution rates, and low expression levels suggesting they are candidates for neofunctionalization. In the end, this thorough study was able to identify evidence supporting many previously proposed evolutionary hypotheses as to the fate of duplicated genes following a WGD. Amanda Wright 2013

5/2013 Thomas Slewinski
Mascheretti, I et al. 2013. Plant Cell 25:404-420
   The WD40-Repeat Proteins NFC101 and NFC102 Regulate Different Aspects of Maize Development through Chromatin Modification

Chromatin remodeling is an essential process required for the initiation and progression of many developmental programs in plants and animals. Changes in the chromatin landscape allow some genes to accessed and expressed while restricting and suppressing others. In this study, Mascheretti et al explore the role of the chromatin modification factors nucleosome remodeling factor complex component101 (NFC101) and NFC102 in floral transition in maize. Analysis of transgenic maize lines that simultaneously down regulated NFC 101 and NFC102 showed that these chromatin remodeling factors act to suppress the expression of Indeterminate 1 (ID1)and Centroradialis8 (ZCN8), two key activators of floral transition. However, modification of the ID1 locus appears to involve the function of Rpd3-type histone deacetylases (HDACs), whereas modification of the ZCN8 locus is HDAC independent. Disruption of the NFC101/NFC102 pathway also resulted in a wide range of developmental defects as well as ectopic tissue specific expression of transposable element repeat nonpolyadenylated RNA. This suggests that NFC101 and NFC102 act though distinct chromatin remodeling mechanisms that regulate multiple pathways during plant development. Thomas Slewinski, 2013

5/2013 Ruairidh Sawers
Peiffer, J et al. 2013. Proc Natl Acad Sci, USA 110:6548-6553
   Diversity and heritability of the maize rhizosphere microbiome under field conditions

The plant rhizosphere microbiome has long been recognized as a key driver of both plant nutrient acquisition and tolerance to biotic and abiotic stress. What is true generally of plant communities is applicable also to crops under agriculture. As interest in lower-input agriculture intensifies, so do efforts to better understand, and ultimately manipulate the microbial community. Such interest notwithstanding, it remains unclear to what extent something of the complexity of a whole community can be the target of agricultural improvement. Here, the authors present a multi-environment field study in which they estimate the sources of variation in maize rhizosphere composition. They report growth of the maize Nested Association Mapping (NAM) founder lines (27 in all including the reference B73) in five field sites: two in the Midwest, three in the Northeast. Root samples were harvested at maturity and microbial diversity estimated by pyrosequencing 16s rRNA amplicons. Although field effects were clearly important in determining the make-up of the rhizosphere community, it is intriguing to note that a small, but significant, effect was observed for maize genetic background. Plants greatly influence their soil environment by secretion of protons, sugars, organic acids, aromatics and enzymes. It seems entirely reasonable that heritable variation in the nature of these exudates impacts the microbial community. The genetic effect, however, showed a strong environmental interaction: the relative ranking of rhizosphere richness among inbred lines varied among the field sites. The authors conclude by speculating on the nature of these effects in landrace and maize wild-relatives. It remains open to debate whether breeding per se, as distinct from shifts in management and adoption of high-input systems, has had an impact on, or in some way limited, the capacity of our crops to interact and benefit from microbial associations. The demonstration of heritable variation in rhizosphere community composition offers a first step to properly address this idea. Ruairidh Sawers, 2012

5/2013 Lewis Lukens
Shen, M, et al. 2013. PLoS One. 8:e57667
   Leveraging non-targeted metabolite profiling via statistical genomics

Metabolomic assays have great power to clarify biological processes, but identifying the compounds that correspond to thousands of mass spectra profiles and elucidating the relationships among the compounds are challenges. In this manuscript, Shen et al. creatively utilize network analyses to characterize the maize seed metabolome. They collect over 8,500 mass spectra profiles from cooked, whole kernals from 210 diverse maize accessions and generate a metabolite network. Modularity is a common property of biological networks. Shen et al. extract groups of metabolites, modules, with abundance levels that are highly correlated across the lines. The modules identified functionally related mass spectra, and the principle of guilt by association helped in the identification of unannotated mass spectra. The 210 accessions have been densely genotyped, and the authors also mapped loci that explain differences in modules across inbred lines. For example, SNPs associated with variants of an alpha-zein seed storage gene correlate with a module including a MS peak likely derived from the protein. This work's novel approaches provide important insights into the organization, diversity and genetic control of the seed metabolome. Lewis Lukens 2013

5/2013 Candice Hirsch
Martin, JA et al. 2014. Scientific Reports 4: DOI: 10.1038/srep04519
   A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

Next generation sequencing has expanded the breadth and depth of questions that biologist are now able to ask. Next generation sequencing has already been used to study the genome, transcriptome, and epigenome of maize and other species. However, as with any technology, it is important to understand both the benefits and limitations of next generation sequencing approaches. In this paper, the authors address an important question relating to consequences of sequencing depth with regards to RNA sequencing (RNA-seq) using extremely deep sequencing of the B73 seedling transcriptome. Among the findings in this paper, the authors show that relative to simulated ???shallow sequencing??? (20 million reads), they were able to detected on average 7,444 more 5b transcripts, and showed that many of the missed transcripts were associated with transcription factor activities. They were also able to improve the current B73 structural annotation including expanding gene models and identifying unannotated genes. This manuscript provides important insights on sequence depth considerations, which in part depends on the scientific goals of that study. Candice Hirsch, 2014.

4/2013 James Schnable
Erhard, KF et al. 2013. Plant Cell 25:808-819
   Maize RNA polymerase IV defines trans-generational epigenetic variation

The c1 (colored alurone1) and pl1 (Purple plant1) genes are two long studied genes involved in the regulation of the pigment anthocyanin in maize. These genes were some of the early "duplicate genetic factors" that first suggested a polyploidy somewhere in the history of maize. As the name suggests, c1 alleles tend to be identifiable by changes in kernel pigmentation, while pl1 alleles result in changes in pigmentation in other tissues like leaves and anthers. While working with a mutant involved in the epigenetic regulation (nrpd1), the authors started to notice purple pigmentation in kernels which became stronger the longer over multiple generations in an nrpd1 mutant background. Afterwards even restoring a wild-type nrpd1 allele did not correct the purple kernels phenotype. The authors verified that the c1 alleles they were working with were truly null alleles and showed expression of the pl1 gene in kernels. After observing this effect in multiple pl1 alleles (but only those which contain transposon insertions upstream of the transcription start site) and similar pigmentation effects in other mutant backgrounds involved in siRNA biogenesis, the authors are able to conclude they have identified an example of transgenerational epigenetic regulation of tissue specific gene expression. While this particular example is dependent on knocking out key elements of maize's epigenetic tool kit, other cases may act as an additional source of heritable variation in maize. James Schnable 2013

4/2013 Ruairidh Sawers
Husakova, E; Hochholdinger, F; Soukup, A. 2013. Ann Bot. 112:417-428
   Lateral root development in the maize (Zea mays) lateral rootless1 mutant

The mutant lateral rootless1 (lrt1) is one of only a handful of known maize root-system-architecture mutants. The mutant was first isolated for the absence of lateral roots during early post-embryonic development. Interestingly, this phenotype can be partially rescued by changing environmental conditions, perhaps most intriguingly by inoculation with mycorrhiza-forming fungi. Here, as part of an Annals of Botany focus issue on Matching Roots to their Environment, the authors provide new detailed histological data on the lrt1 phenotype. Consistent with the earlier observations of an environmentally sensitive phenotype, the authors propose that the lrt1 mutant does not affect the frequency of lateral root primordia formation per se; rather that, under standard conditions, mutant primordia arrest early during development, most commonly during root emergence. The authors hypothesise that this arrest is a result of a failure to penetrate unprepared surface cell-layers in the primary root. In support of this model, the authors report impaired root meristem function coupled with a disruption of both epidermal and sub-epidermal cell layers. In addition, they observe ectopic lignification and deposition of poly-phenolics in just those surface root layers through which lateral roots would emerge in a wild-type plant. While the lrt1 mutant is still to be cloned, evidence continues to accumulate to suggest that the gene plays a role beyond blind development, and that it has a function in the integration of environmental and developmental signals. Ruairidh Sawers, 2013

4/2013 Lewis Lukens
Massman, J; Jung, H; Bernardo, R. 2013. Crop Sci. 53:58-66
   Genomewide Selection versus Marker-assisted Recurrent Selection to Improve Grain Yield and Stover-quality Traits for Cellulosic Ethanol in Maize

Selection of plants that exhibit certain favorable traits has been largely responsible for steady improvements in agricultural productivity. Marker assisted selection (MAS) and more recently genomic selection (GS) methods utilize plant genotypic information to inform the selection process. Two key benefits of selection based on genotype instead of phenotype are that young plants can be assayed and expensive trait measurements can be avoided. Marker assisted selection involves identifying a set markers that are significantly associated with a trait and using information from these markers to guide selection. Genomic selection also uses marker genotypes to predict performance but simultaneously estimates the effects of all markers. Here, Massman et al. compare the effectiveness of MAS and GS in improving maize hybrid yield and stover-quality traits important for cellulosic ethanol production. They first performed one round of phenotypic selection on stover and stover + yield indices calculated from observed traits. They then performed two cycles of MAS and GS, selecting on predicted index values. GS resulted in larger index gains than did MAS over the three cycles of selection. Interestingly, however, individual stover and yield trait values largely did not improve in populations that had undergone GS or MAS relative to the initial population obtained through phenotypic selection. This result may have been due to the selection on indices rather than on individual traits. Although a number of studies have demonstrated the superiority of GS relative to MAS in simulations and cross-validation studies, this work provides an interesting empirical comparison of the methods and highlights the promise of GS. Lewis Lukens 2013

4/2013 Amanda Wright
Maron, LG et al. 2013. Proc Natl Acad Sci, USA 110:5241-5246
   Aluminum tolerance in maize is associated with higher MATE1 gene copy number

Although copy number variation (CNV) between maize inbred lines is extensive, increasing or decreasing the copy number of a specific gene has rarely been linked to a phenotype. Maron et al. discovered that maize lines containing three copies of MATE1 have an increased aluminum tolerance relative to maize lines with only one copy. MATE1 is a transporter that moves citrate out of roots cells and into the rhizosphere where the citrate can complex with Al preventing the uptake of Al into root cells. MATE1 had previously been correlated with a QTL detected in a mapping population created by crossing an Al sensitive to an Al resistant line, but the molecular mechanism of the MATE1 associated resistance was unclear. A functional study showed that MATE1 proteins from the resistant and sensitive lines transport citrate equivalently ruling out amino acid changes as the cause of the Al tolerance. FISH suggested that there may be more than one copy of MATE1 at the end of chromosome six and this was confirmed by qPCR and by sequencing the region. The increase in MATE1 copy number results in an increase in expression of MATE1. Sequencing showed that a highly similar 30 kb genomic region, which contains only the MATE1 gene and multiple retrotransposons, is triplicated in the Al tolerant line. The lack of sequence diversity between the repeats suggests that the triplication was a recent event possibly occurring since domestication. After screening a diverse panel of 167 inbred and teosinte lines, the MATE1 triplication was identified in two additional inbreds, which are also Al tolerant. The three lines that contain the MATE1 triplication originated in a region of South America with acidic soils. Acidic soils increase the toxicity of Al and acidic soil tolerance is a desired trait in South American breeding programs. Amanda Wright 2013

3/2013 Ruairidh Sawers
Bommert, P; Satoh-Nagasawa, N; Jackson, DP. 2013. Nature Genetics. 45:334-7
   Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus

The ear of modern maize is one of the most striking examples of domestication at work, and, perhaps not surprisingly, the loci controlling variation in ear architecture have been a target of genetic study from the time of the first experiments to understand the differences between maize and teosinte. Despite this long history of investigation, the underlying genes controlling ear architecture have remained broadly unknown. Now, in their article, Bommert et al. demonstrate that single-nucleotide polymorphisms in the gene Fasciated Ear2 are sufficient to result in an increase in row number in the W22 background. Significantly, this increase in rows is accomplished without the loss of row-ordering typical of the previously characterized null mutants. The authors go on to present a model for their observations based on changes in inflorescence meristem size. Where the teosinte ear has 2 rows of kernels, early domesticates quickly developed multiple kernel rows, from the basic 8-row types (actual row number varies), such as Nal-Tel, for which the ear architecture of early specimens is wonderfully preserved in pre-Colombian ceramics, through to the high-row numbers of the small-grained ancient popcorns, such as Palomero Toluqueno. While Bommert et al. do not present evidence for the involvement of Fasciated Ear2 in this early diversification, they do suggest that variation in the gene played a role in later line improvement. Ruairidh Sawers, 2013

3/2013 Lewis Lukens
Udy, DB et al. 2012. Plant Physiol 160:1420-1431
   Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize

In early maize leaf development, chloroplastic DNA (cpDNA) accumulates to high levels. One reasonable explanation for this phenomenon is that a high cpDNA copy number generates abundant RNA that in turn facilitates the massive biogenesis of photosynthetic enzyme complexes. Here, Udy et al. discover that mutations in a nuclear encoded, predicted organellar DNA polymerase are responsible for a number of white2 (w2) maize mutants with pale green to white leaves. Plants homozygous for a weak w2 allele have very pale yellow green leaves. Plants homozygous for a strong w2 allele are albino. The weak and strong mutant alleles cause about a 5 fold and 100 fold decrease in chloroplast DNA copy number, respectively. Udy et al. find that in early leaf development, a number of chloroplast encoded RNAs are reduced roughly proportionally to the DNA reduction. Thus, DNA copy number does appear to limit the abundance of a number of RNA transcripts. Nonetheless, other genes' transcripts are less sensitive to the loss of plastid DNA, and rpoB RNA is elevated despite DNA loss. The authors also investigate the abundance of photosynthetic enzyme complex subunits within the weak, w2 mutant. The reduction of protein abundances within the mutant exceeds the reduction in chloroplast RNA abundance, indicating that different chloroplast RNAs interact synergistically to affect protein levels. Overall, this work paints an intriguing picture of how chloroplast DNA copy number affects chloroplast RNA, photosynthetic enzyme complexes, and leaf appearance. Lewis Lukens 2013

3/2013 James Schnable
Mauro-Herrera, M et al. 2013. G3 3:283-95
   Genetic control and comparative genomic analysis of flowering time in setaria (poaceae)

Studies of quantitative traits are widely used across many species to examine traits ranging from morphology, secondary metabolite production, stress resistance, and yield (as well as many others). The identification of QTLs allows researchers to study the sources of existing natural variation and acts as a complement to studies of mendialian mutations. However, until recently, and unlike mendelian genetic studies, comparisons of the loci underlying quantitative variation among different species have been rare. Mauro-Herrara et al demonstrate a straightforward approach to interspecies comparisons of QTL studies. In the paper the authors using a population of recombinant inbred lines to identify a set of major QTL responsible for the variation in flowering time between domesticated Setaria italica and its wild ancestor Setaria viridis. They then employed a synteny-based approach to compare their results to previous studies of variation in flowering time in maize and sorghum. While several QTLs are conserved among these species (which diverged ~25 million years ago) the authors are able to conclude that the major flowering time QTL identified on maize chromosome 10 is maize-specific. James Schnable 2013

3/2013 Thomas Slewinski
Xu, Z et al. 2013. Crop Sci 53:735-745
   The Realized Yield Effect of Genetically Engineered Crops: U.S. Maize and Soybean

Patenting and growing genetically engineered (GE) crops, as well as labeling the food products that contain them, have been at the forefront of recent political and legislative decisions in the US and many other countries. But what are the realized yield effects of GE on agricultural production? This is the issue that truly underpins their widespread adoption and use in the first place. Xu et. al. investigate whether and to what extent GE crops have impacted realized yields by analyzing historical data from non-irrigated maize and soybean in the U.S. from 1964-2010. They found that GE technology did confer an increase in realized yields, as well as a strong trend in yield growth in both crops. GE varieties of maize had the largest increase in realized yields, with the most significant gains in the Central Corn Belt. However, data from GE varieties of soybean implicate a slight yield drag. Overall these data highlight an encouraging trajectory for GE technology, mainly because first generation transgenic traits were designed to protect the yield and yield potential of their hybrid background, not increase yield per se. Although, the trends forecasted from these data suggest that projected yield gains made by first generation transgenic traits will fall short of the accelerated demands humans will put on agriculture. Thus new and novel GE traits, outside the realm of protection technology, will most likely be needed to boost yields beyond currently projected production capacity. Tom Slewinski, 2013

2/2013 Amanda Wright
Moon, J; Candela, H; Hake, S. 2013. Development. 140:405-412
   The Liguleless narrow mutation affects proximal-distal signaling and leaf growth

A recent paper from the Hake group reports the characterization and cloning of Liguleless narrow-R (Lgn-R), a semi-dominant maize mutant that affects leaf development. Lgn-R plants have a number of phenotypes including defects in auricle and ligule formation that occur because the blade-sheath boundary is not correctly specified. The kinase activity of LGN is disrupted in the mutant leading to a reduced expression of liguleless1 and liguleless2, two genes previously identified as important for ligule formation in the developing leaf. Further analysis of the Lgn-R mutant suggests that LGN is needed to transmit the blade-sheath boundary signal past the midrib to the margins of the leaf. In addition to emphasizing the utility of the maize leaf as a system for studying cell fate specification and other developmental processes, this paper also includes interesting insights into the cloning process and the search for additional alleles of Lgn. The authors used whole genome sequencing to confirm that no other genes were mutated in the Lgn mapping interval suggesting that the era of cloning by genome or transcript sequencing is almost upon us. Amanda Wright 2013

2/2013 Lewis Lukens
Goettel, W; Messing, J. 2013. Theor Appl Genet. 126:159-177
   Paramutagenicity of a p1 epiallele in maize

Paramutation is a fascinating phenomenon in maize genetics. Paramutation may occur between two alleles with identical nucleotides but differing in epigenetic state. In the heterozygote, one allele, the paramutagenic allele, can heritably silence the second, paramutable allele. The paramutable allele after exposure to the paramutagenic allele is termed the paramutant allele. Repetitive sequences are often associated with paramutation, and mutations in genes that function within the RNA directed DNA methylation pathway can disrupt paramutation. In this paper, the authors investigate the interaction and inheritance of P1-pr alleles with P1-rr alleles. The P1-pr allele produces a patterned pericarp, and the P1-rr allele produces a dark red pericarp. They find that in a heterozygote, the P1-pr allele represses the P1-rr allele. Interestingly, the repression is highly variable- hybrid seed ranges from nearly colourless to dark red. The pigmentation of ears from testcross plants derived from F1 plants correlated with the pigmentation of the hybrid ears. Thus, different epigenetic states of the paramutant allele within the hybrid population were transmitted through meiosis. The authors also analyze cytosine methylation within upstream regulatory sequences containing p1 specific repeat and transposon sequences. Among F1 plants with variable pigmentation, cytosine methylation levels within the p1 repeats was similar, although nominally higher among those plants with little colour. Among testcross populations of F1 plants, the average methylation of p1 cytosines correlated with the absence of pigment. This work underscores how repeat-associated epigenetic changes can generate a range of novel traits and suggests that paramutation may be triggered by transposons adjacent to regulatory sequences. Lewis Lukens 2013

2/2013 Ruairidh Sawers
Hufford, MB et al. 2012. PLoS One 7:e47659
   Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight

The story of maize domestication remains a source of fascination, both for specialists and the broader public alike. A potent combination of genetics and archaeology has provided us with an increasingly clear picture of the development of maize from wild Balsas teosinte, at a period approximately 9000 years-ago, in the lowlands of the Balsas river valley, in western Mexico. Nonetheless, as Hufford et al. point out, our understanding of the ecological context of maize domestication is far less complete. Here, the authors use climatic modelling to estimate the historical distribution of selected ancient maize land-races, the ancestral Balsas teosinte, and the related Chalco teosinte, and observe ancient patterns of distribution consistent with current scenarios of domestication. In addition, while the distributions of the two teosintes have changed over time, they have remained complementary, the two sub-species occupying what the authors refer to as restricted and highly contrasting ecological niches. In contrast, both the archaeological record and the authors simulations agree that early domesticated maize spread rapidly from the regions occupied by its progenitor Balsas teosinte, into areas occupied by Chalco teosinte, and rapidly adopted a distribution broader than either of these wild sub-species. The forces behind such rapid ecological expansion are of both tremendous historical interest and modern relevance. Previous studies have suggested that substantial genetic introgression has occurred from Chalco teosinte to domesticated maize, an intriguing avenue for the acquisition of adaptive variation linked to niche expansion. Here, the authors develop the idea of domesticated maize playing a role as a genetic bridge between the two teosinte species, facilitating gene flow that would have been limited historically given complementary distribution patterns. And, clearly, the cultural influence of the first maize farmers and breeders must also be taken into account. Ruairidh Sawers, 2013.

2/2013 Thomas Slewinski
Sekhon, RS et al. 2012. Plant Physiol 159:1730-1744
   Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize

Sink-source interactions underpin all aspects of growth and yielding capacities in crop plants. Initiation of leaf (source) senescence is coordinated with final phases of grain (sink) filling. This process recycles resources in the leaf and directs them toward the grain. In this study, the authors analyzed natural and sugar-induced (by pollination prevention) senescence in leaves and internodes using transcriptional and metabolic analysis. The authors found that similar senescence processes in leaves are later recapitulated in the internodes, supporting the hypothesis that leaf senescence is developmentally coordinated with other plant organs. Interestingly, in the non-pollinated plants, metabolic changes in leaves, such as increased carbohydrate content, can be detected a week after anthesis but global transcriptional reprogramming does not occur until 24 to 30 days after anthesis, revealing a substantial buffering capacity in the senescence process. However, differences between natural and sugar induced senescence were detected. A subset of senescence-associated genes (SAGs), ethylene, JA and salicylic acic biosynthetic genes were up-regulated in natural senescence, but unaltered in the sugar-induced senescence. This suggests there are some key differences between the two senescence induction pathways. Investigations such as this will help to identify new gene targets that control agronomically important traits where accurately timed senescence is critical - including stay green, days to harvest, and harvest index. Thomas Slewinski 2013

2/2013 James Schnable
Li, L et al. 2013. PLoS Genetics 9:e1003202
   Mendelian and non-mendelian regulation of gene expression in maize

The Intermated B73 x Mo17 population (IBM) is a set of recombinant inbred lines that have been widely used in maize quantitative genetics studies for more than a decade. This paper reports on the analysis of gene expression levels (quantified using RNA-seq) in 105 lines selected from this population. These data allowed the identification of cis- and trans- regulatory variation effecting the expression of more than 19,000 maize genes. The authors also uncovered evidence of a number of other unexpected patterns of gene regulation including paramutation-like patterns of expression. In a number of cases the expression of non-syntenic genes (often associated with CACTA transposons) are correlated with reductions in the expression of homologous genes at ancestrally conserved syntenic locations. This suggests exotic sequences captured by transposons can interfere with the expression of the original gene, potentially acting as a source of novel regulatory function. The ability to look up the mapped locations of trans-eQTLs regulating specific genes using the included supplementary data may be of interest to the greatest number of individual researchers. James Schnable, 2013

1/2013 James Schnable
Boerner, S; McGinnis, K. 2012. PLoS One 7:e43047
   Computational identification and functional predictions of long noncoding RNA in Zea mays

Long noncoding RNAs behave in many ways like traditional genes often showing similar patterns of chromatin state and sequence conservation as observed for protein-coding genes. Many of these long noncoding RNAs appear to function in the regulation of either chromatin states or gene expression, however most of the genome wide studies conducted to date have focused on mammalian systems. This study used two different computational approaches to identify maize transcripts unlikely to code for protiens. Unlikely mammalian systems where nearly half of unique transcripts appear to be non-protein-coding, more than six out of seven maize transcripts apparently codes for protein. Any analysis where plant genomes appear to be globally different from mammalian genomes is interesting, however this paper also brings up an important issue for maize researchers to be aware of in the current set of maize gene model annotations. Four-hundred and seventy of the long noncoding transcripts identified in this study corresponded to sequences in the maize genome currently annotated as protein-coding genes (with short ORFs and no homology to any known sequence). This suggests maize researchers who identify candidate genes with small ORFs and no homology should be cautious about assuming these genes code for protein at all. James Schnable, 2013

1/2013 Thomas Slewinski
Zhang, X et al. 2012. Plant Cell 24:4577-4589
   Identification of pan2 by quantitative proteomics as a leucine-rich repeat-receptor-like kinase acting upstream of pan1 to polarize cell division in maize

Polarized and asymmetric cell divisions underlie many aspects of plant development. Unequal cell division can give rise to daughter cells with distinct cell identities that govern subsequent cell fates - as in the case of stomata and flanking subsidiary cell formation in the maize leaf epidermis. Pangloss1 (PAN1) was previously identified as a kinase-dead Leu-rich repeat-receptor-like kinase (LRR-RLK) involved in stomatal development by promoting the polarization o f the subsidiary mother cell (SMC) division towards the adjacent guard mother cell (GMC). In this article, the authors describe the identification, cloning and genetic interactions of Pangloss2( PAN2), a second gene that functions in polarization and development of the SMC. Using a combination of quantitative proteomics and bulk segregate mapping, the authors identified PAN2 as a second kinase-dead LRR-RLK. Localization and interaction studies reviled that PAN2 is required for, and co-localizes with PAN1, although the two proteins do not directly interact. Along with the synergistic interaction observed in the double mutants, the authors propose that PAN2 acts first in the cascade of events that leads to SMC formation and functions cooperatively or is partially redundant with PAN1 to perceive or amplify positional cues from the GMC. Importantly, this study also highlights how new technologies, such as quantitative proteomics, can be integrated into forward genetic approaches in order to elucidate gene identity and function, Thomas Slewinski, 2013

1/2013 Lewis Lukens
van Heerwaarden, J et al. 2012. Proc Natl Acad Sci, USA 109:12420-12425
   Historical genomics of North American maize

Genetic improvement in maize has been a remarkable success, accounting for much of the roughly doubling of maize yields in the last 80 years. Heerwarden et al. analyzed genome-wide SNP variability from 400 maize accessions - including open pollinated landraces, early inbred lines, advanced public inbred lines, and elite commercial inbred lines- to investigate the genomic changes that have occurred as a result of this selective breeding. Breeding increasingly differentiated the heterotic groups, genetically distinct breeding pools that are crossed to make hybrid seed. However, overall allele frequencies have remained remarkably constant across breeding history. Some loci show strong shifts in frequency indicative of directional selection across time. However, the selection candidates did not have long, shared haplotypes, reduced haplotype diversity, or evidence of different ancestry relative to other regions of the genome. The authors conclude that directional selection has led to shifts in population structure, but dramatic genomic change has not accompanied the remarkable genetic improvements in crop productivity. Lewis Lukens 2012

1/2013 Ruairidh Sawers
Wang, H; Bennetzen, J. 2012. Proc Natl Acad Sci, USA 109:21004-9
   Centromere retention and loss during the descent of maize from a tetraploid ancestor

Comparative analysis of genetic and physical maps of the grasses has established that the modern maize genome derives from an ancient tetraploid ancestor. In the ~12 million years that have elapsed since this tetraploid event, large scale rearrangements have returned the genome to a diploid form, while events at the gene level have resulted in the loss of one copy of many duplicate genes, a process known as fractionation. The maize tetraploid event occurred soon after the split between the maize and sorghum lineages. Consequently, the availability of sequenced maize and sorghum genomes provides a wonderful opportunity to capture a genome in flux as it reorganizes following tetraploidy. Schnable et al. (Proc Natl Acad Sci, 2011) have exploited previously genomic resources to follow fractionation in maize, and to define the ancestry of the modern genome with respect to the two ancestral genomes of the tetraploid ancestor. Here, Wang and Bennetzen address a fundamental process required for a tetraploid to return to the diploid state, namely, reduction of chromosome number driven by reorganization of the centromeres. Making use of single-copy pericentromeric sequences conserved between maize and sorghum, the authors provide evidence for whole chromosome insertion near, but not necessarily into, other centromeres, along with translocation and fusion events, and generate a scenario for the establishment of modern maize genome organization. While we now have a far better understanding of the end-point if this process, the authors acknowledge the potential mechanistic problems of passing through the intermediate steps: notably, stability of dicentric chromosomes would require rapid inactivation of one of the two centromeres. Furthermore, what might we expect of the many intermediate forms between tetraploidy and the modern diploid state? And, what are the forces that have driven this remarkable return to the ancestral karyotype? Ruairidh Sawers, 2012.

1/2013 Amanda Wright
Guan, JC et al. 2012. Plant Physiol 160:1303-1317
   Diverse roles of strigolactone signaling in maize architecture and the uncoupling of a branching-specific sub-network

The plant hormone, strigolactone (SL), induces the germination of Striga sp. parasite plants and is required for establishing symbiotic mycorrhizae relationships. In addition to these roles, mutant analysis in diverse plant species has shown that SL signaling inhibits lateral branching. To investigate the role SL plays in establishing maize plant architecture, Guan et al. identified a mutant that disrupts carotenoid cleavage dioxygenase8 (ccd8), a SL biosynthetic gene. While ccd8 mutants have twice as many axillary branches as wild-type plants, the branching phenotype is minor compared to that seen in SL pathway mutants in pea, Arabidopsis, and rice. In pea and Arabidopsis, SL signaling activates teosinte-branched1 (tb1) homologues, which inhibits branching. In contrast, expression and tb1; ccd8 double mutant analysis showed that SL does not regulate tb1 in maize. Careful study of the ccd8 mutant phenotype revealed that in addition to branching, SL signaling regulates plant height, stem diameter, nodal (adventitious) root system formation and inflorescent development in maize. The authors suggest that while ccd8 was not a good domestication target in maize because it is single copy and has the associated pleiotropic phenotypes, SL signaling components maybe domestication targets in other grasses. Amanda J. Wright 2013

12/2012 David Braun
Kelliher, T; Walbot, V. 2012. Science. 337:345-348
   Hypoxia triggers meiotic fate acquisition in maize

Through confocal microscopy Kelliher and Walbot traced cellular ontogeny through multiple rounds of cell division to construct a three-dimensional model of a growing anther. From these studies, they determined when and where during anther development cells switch from a somatic to germinal developmental program. Using this framework, the authors characterized male development in a couple of mutant backgrounds. The multiple archesporial cells1 (mac1) mutant displays altered cell patterning during anther development, misspecification of cell identity, and male sterility. Another male sterile mutant, male sterile converted anther1 (mcsa1) was found to be epistatic to mac1. MSCA1 encodes a glutaredoxin, which is proposed to function as a redox regulator. During anther development, the tassel is tightly wrapped in ensheathing leaves and the oxygen content in the tissue is hypoxic, with approximately 1.2-1.4% oxygen. By applying nitrogen or oxygen gasses through hoses connected to fine needles directly to the developing tassel, Kelliher and Walbot observed changes in anther cell identity and were able to partially rescue the mcsa1 mutant phenotype. They proposed that the oxygen status experienced by cells within the developing anther serves as a positional cue to specify germ cell fate. This research highlights how the environment (here the oxygen content in a tissue) can trigger cell specification and reprogram plant development. David Braun, 2012

12/2012 Addie Thompson
Schnable, J; Freeling, M; Lyons, EH. 2012. Genome Biology and Evolution. 4:265-77
   Genome-wide analysis of syntenic gene deletion in the grasses

An ancient whole-genome duplication event occurred in the grasses prior to the divergence of the major lineages. Following this polyploidy, many duplicate gene copies were lost through fractionation. After identifying syntenic blocks, rates of duplicate gene loss can be compared. This has been done in maize, where a more recent WGD event has taken place since the all-grass duplication discussed here. Gene retention has been shown to be more frequent for protein complexes, transcription factors, and conserved non-coding regulatory elements. A bias in gene loss between duplicated regions is also present. Here, a method for identifying syntenic blocks and lost orthologs and assigning fractionation regions and bias is detailed by example of the ancient grass duplication. Analysis showed that ongoing fractionation in the grasses is still biased, and furthermore, that reciprocal duplicated gene loss does not seem to have caused the adaptive radiation of the grass lineages. Not only does this work provide a resource for scientists seeking ways to study ancient polyploidy and subsequent fractionation, but it provides a dataset of high confidence syntenic orthologs in other grasses which could be helpful to maize researchers. Addie Thompson, 2012

12/2012 Liza Conrad
Slewinski, TL et al. 2012. Plant Cell Physiol 53:2030-2037
   Scarecrow plays a role in establishing Kranz anatomy in maize leaves

The C4 photosynthetic pathway is characterized by the separation of CO2 fixation and the Calvin cycle into two distinct cell types, the mesophyll (M) and bundle sheath (BS). The arrangement of BS and M cells in concentric rings around the veins is known as the Kranz anatomy. This study implicates the SCARECROW (SCR) transcription factor in the structural specification of the Kranz anatomy in maize leaves. Loss of SCR results in abnormal BS and veins in maize leaves. Previously, SCR has been shown to function in endodermal differentiation in roots and shoots. Evidence suggests conserved pathways may be involved in the differentiation of both endodermis in roots and BS cells in leaves. This includes the shared expression pattern of the PIN1 auxin transport gene in both the root endodermis and BS cell. The authors suggest that it is possible ZmSCR functions in developing leaf primordia to restrict the movement of SHORTROOT to the cells that will become BS. Liza Conrad, 2012

12/2012 Beth Thompson
Huang, JT; Dooner, HK. 2012. Plant Cell 24:4149-4162
   The spectrum and frequency of self-inflicted and host gene mutations produced by the transposon Ac in maize

The study of transposition has a long and distinguished history in maize, starting with the pioneering work of Barbara McClintock. Transposons are now appreciated as major generators of mutation and driving forces of evolution, although major questions remain about the type and frequency of mutations and chromosomal rearrangements that can be generated by transposons. A recent paper by Huang and Dooner, investigates mutations caused by the autonomous Activator transposon, focusing the less common classes of mutations that are not caused by simple excision. Previous work to estimate Ac mutation rates employ systems in which Ac is inserted in the coding region of a gene. In these systems, imprecise excisions as well as other more complex mutations result in loss-of-function phenotypes. Because simple excisions greatly outnumber more complex mutations, characterizing and estimating rates of these more complex mutations has been challenging. Here, the authors utilize a clever system in which Ac is inserted in the 5 UTR of bz, in which simple excision events create purple revertants, while host or transposon deletions produce stable bronze revertants. They isolated 72 stable bronze derivitives, most of which turned out to be internal Ac deletions that behaved as new Ds elements. Interestingly, mutations rates of Ac to Ds in this system were estimated to be an order of magnitude higher than previous estimates. The second most abundant class of mutations were fractured Ac elements, which in which either the 5 or 3 end of Ac was deleted. The abundance of this class of mutations was somewhat surprising given the few examples present in the literature. They also found several deletions of adjacent host sequences (with or without Ac) and single events of other mutation classes. Characterization of these complex mutations indicate most likely originate by DNA repair synthesis followed by microhomology-mediated end joining. Beth Thompson, 2012

12/2012 Owen Hoekenga
Burt, AJ et al. 2012. Crop Sci 53:554-563
   Development and utilization of high carotenoid (HiC) maize germplasm: Proof of concept

Translational genomics is one of those buzz phrases tossed about by funding agencies, college deans and other decision makers who are looking for ways to move from laboratory to farm to table. Plant breeders have been using translational genomics since the birth of the discipline, applying basic scientific knowledge to improve quality of life for consumers. Plant biotechnology is an area where translational genomics can easily be applied, but we most often think of transgenic crop improvement in this arena. Certainly, transgenic traits that serve producer needs (e.g. herbicide resistance) have been key developments for agriculture at the turn of the 21st Century, but new innovations to better serve consumer needs should be just around the corner. An obvious one is enhancing nutritional quality for key nutrients, such as dietary carotenoids, which can take place either by using transgenic or conventional breeding based approaches. One of the key issues raised in the present study is the use of animal feeding trials to verify that the predicted improvement in nutrient concentration actually translates into enhanced animal health and/or product quality. Here, high carotenoid maize lines developed using conventional breeding are evaluated using feeding studies with laying hens, to validate observations made by eye on kernel color and by HPLC for carotenoid profiling. It was not unexpected that a poultry diet supplemented with carotenoids from marigolds had higher total carotenoids and lutein than any other diet. However, it was very encouraging to see that the experimental maize varieties out delivered zeaxanthins, which together with lutein help protect us from macular degeneration. While this is clearly just a proof of concept, this early test makes clear the promise of translational genomics towards enhancing nutritional quality and human health. Perhaps equally importantly, consumers are already prepared to pay premiums for eggs with enhanced nutritional qualities (e.g. omega-3 fatty acids), such that we know that the marketplace is willing to accept such a product. Owen Hoekenga, 2012.

11/2012 Addie Thompson
Sekhon, RS; Wang, P; Sidorenko, LV; Chandler, V; Chopra, S. 2012. PLoS Genetics. 8:e1002980
   Maize Unstable factor for orange1 is required for maintaining silencing associated with paramutation at the pericarp color1 and booster1 loci

Paramutation is the heritable expression change of one allele due to the epigenetic influence of another allele, leading to non-Mendelian inheritance of the affected traits. Though the epigenetic mechanisms of allelic diversity are just starting to emerge in recent research, several factors have been implicated in contributing to the presence and regulation of paramutation in maize, including upstream tandem repeats and RNA-mediated silencing mechanisms. By characterizing one paramutagenic and one non-paramutagenic epiallele of the pericarp color1 gene, Rajandeep et. al. demonstrate that asymmetric (CHH) and not symmetric (CG, CHG) methylation differ in an enhancer element of the gene. This supports the idea that RNA-mediated silencing pathways play a role in paramutation at p1. A dominant mutation at unstable factor for orange1 (ufo1) leads to reactivation of the silenced epialleles, as well as the loss of H3K9me2, a suppressive histone methylation that may be maintaining silencing. ufo1 is also shown to be required for silencing at another paramutable locus in maize, booster1. This paper serves to further implicate RNA-mediated silencing mechanisms in paramutation, as well as to characterize mutations and epialleles of genes involved in epigenetic silencing and paramutation. Addie Thompson, 2012

11/2012 Owen Hoekenga
Heffner, EL; Lorenz, Aaron J.; Jannink, J; Sorrells, ME. 2010. Crop Sci. 50:1681-1690
   Plant Breeding with Genomic Selection: Gain per Unit Time and Cost

I apologize for the mistake I made back in September, claiming to have introduced and discussed a concept when in fact I had not. To remedy this omission, genomic selection is a novel approach to marker assisted selection wherein as much information as feasible is integrated into a single, cohesive framework to advance the breeding program. Typically, marker assisted selection programs rely on relatively few genetic markers and do a reasonable job at capturing and following modest to large effect quantitative trait loci (QTL). However, small effect QTL are often difficult to follow but make up a majority of the genetic bases for many traits. Genomic selection uses dense, genome-wide markers to build a statistical model that includes both small and large effect QTL. This model allows one to predict phenotypic outcomes for individuals within a breeding program, such that one relies on the prediction to make the selection rather than using phenotypic evaluation. First pioneered in cattle, genomic selection allows a massive savings in time and effort in exchange for an increased workload in the marker lab. This paper summarizes cost/benefit analyses for marker assisted selection and genomic selection-based breeding programs in maize and wheat, to help convince a broad audience of the utility of this improved method of selection. Owen Hoekenga 2012

11/2012 Liza Conrad
Dahal, Diwakar; Mooney, B; Newton, K. 2012. Plant J. 72:70-83
   Specific changes in total and mitochondrial proteomes are associated with higher levels of heterosis in maize hybrids

The mechanism underlying heterosis is poorly understood although it has been hypothesized that mitochondrial respiration plays an important part. This study compared total and mitochondrial protein fractions from ear shoots in two higher-heterosis hybrids to a lower-heterosis hybrid. Overall, only 2-3% of proteins observed changed expression between higher- and lower-heterosis hybrids. Changes in energy metabolism proteins involved in glycolysis, the TCA cycle, photorespiration and ETC were correlated with higher-heterosis hybrids. Additionally, a differential abundance of stress-related proteins was detected in these higher-heterosis hybrids. Interestingly, it was demonstrated that the total amount of certain proteins did not change but rather different isoforms correlated to differences in heterosis. These data suggest higher-heterosis hybrids have more efficient energy metabolism and are better adapted to various stresses thus increasing their vigor and level of heterosis. Liza Conrad, 2012

11/2012 David Braun
Slewinski, TL et al. 2012. Plant Physiol 160:1540-1550
   Tie-dyed2 encodes a callose synthase that functions in vein development which affects symplastic trafficking within the phloem of maize leaves

Mutant leaves of tie-dyed2 (tdy2) plants are variegated and exhibit distinct regions of either normal-appearing green tissue, or yellow tissue that hyperaccumulates starch and soluble sugars. To understand the basis for this carbohydrate partitioning defect, Slewinski et al. phenotypically characterized the phloem transport capacity of the tdy2 mutant and cloned the corresponding gene. Tdy2 encodes a callose synthase that is expressed in leaves, roots, stems, tassels, and ears. RNA in situ hybridization experiments determined that the gene is expressed in the procambium of the earliest initiated leaves, and throughout the developing veins in slightly older leaves. To characterize the impediment to sucrose transport in tdy2 mutant leaves, 14C-labeled sucrose was applied to tdy2 yellow leaf regions and wild-type leaves. These experiments showed that the mutant was defective in phloem export. However, application of 14C-sucrose to green regions of tdy2 leaves located distal to yellow tissue demonstrated that long-distance transport through the phloem was not impaired. Because Tdy2 is expressed during early vein development and the tdy2 mutant is disrupted in sucrose phloem export, transmission electron microscopy was used to investigate vein ultrastructure. These experiments revealed that tdy2 yellow leaf regions have incomplete vein maturation, but normal plasmodesmata ultrastructure and frequency. Furthermore, because the companion cells in tdy2 yellow leaf regions contain massive oil droplets, a storage form of carbon, these studies implicated a defect in cell-to-cell solute transport from the phloem companion cells to sieve elements. Hence, Tdy2 function is required for proper vein development and ultimately for symplastic trafficking into the phloem translocation stream. David Braun, 2012

10/2012 Liza Conrad
Wang, P et al. 2013. Planta 237:481-495
   Evolution of GOLDEN2-LIKE gene function in C3 and C4 plants

C4 plants, such as maize and Sorghum, have dimorphic chloroplasts, bundle sheath (BS) and mesophyll (M) cells, while C3 plants have a single chloroplast type. The two paralogous GOLDEN2-like (GLK) genes in maize, ZmG2 and ZmGlk1, are expressed in a BS or M cell-specific manner. This study investigates the evolution and sub-functionalization of the GLK gene family. Phylogenetic analysis including 50 GLK genes revealed that the last common ancestor of flowering plants had a single GLK gene therefore gene duplications have occurred in a lineage specific manner. However, all C4 species have two GLK genes while C3 plants can have either one or two copies. Expression of the two GLK genes present in sorghum is compartmentalized similarly to maize although strong compartmentalization is not found in C4 eudicot Cleome gynandra that has morphologically similar BS and M cells. To determine whether the sub-functionalization present in maize and sorghum is a common feature of all Poales, GLK single and double mutants were generated in rice, a C3 plant. Phenotypic analysis demonstrated both GLK genes in rice regulate chloroplast development in both BS and M cells in a functioning redundantly manner. Taken together with lack of compartmentalization in C. gynandra, this suggests GLK compartmentalization may be restricted to only C4 species with dimorphic chloroplasts. The authors hypothesize that duplication of GLK genes allows for sub-functionalization leading to to cell-specific function of BS and M cells in C4 plants with dimorphic chloroplast. Liza Conrad 2012

10/2012 Owen Hoekenga
Morohashi, K, et al. 2012. Plant Cell. 24:2745-64
   A genome-wide regulatory framework identifies maize pericarp color1 controlled genes

Pigments offer powerful reporter systems for genetic research. Pigments, such as the phenylpropanoid-derived phlobaphenes, are highly visual such that small changes to regulatory or structural genes are obvious but often dispensable to the health of a plant. The Pericarp color1 (P1) locus regulates both phlobaphene pigments in the pericarp and structurally related insecticidal maysins in silks. Thus, the P1 regulon represents study systems of both basic and applied biological interest. Here, a systems biology approach was used to more completely describe the P1 regulon, combining next generation sequencing based approaches to examine gene expression and where transcriptional regulators such as P1 bind within chromatin. Taken together, these lines of evidence point to the genes that P1 regulates (or is at least physically associated with) using functional (P1-rr) and null (P1-ww) alleles in both pericarp and silk tissues. P1 had a much larger regulatory impact than anticipated by visual inspection of the isogenic mutant and wild-type stocks. More than 3300 genes were differentially regulated in pericarp between P1-rr and P1-ww sibling lines, with 16/18 representative genes confirmed by qRT-PCR. More than 2100 genes were differentially regulated in silks. These targets included the expected phenylpropanoid-related genes, but also included carbohydrate and lipid metabolic genes and other even less obviously connected pathways. Chromatin immunoprecipitation experiments identified many of the same genes identified by RNA-Seq; however, the number of genes in common to both analyses was similar to that fraction expected by chance. Perhaps more importantly, the canonical transcription factor-binding motif for P1 was highly enriched in both positively and negatively regulated loci, suggesting that the systems biology outcomes were consistent with our existing body of knowledge. This study demonstrates the clear potential of systems biology approaches, to integrate transcriptomic, biochemical and genetic lines of inquiry into a single comprehensive view of a question that has been under examination for more than 100 years. Owen Hoekenga 2012

10/2012 Beth Thompson
Takacs, EM et al. 2012. Plant Cell 24:3219-3234
   Ontogeny of the Maize Shoot Apical Meristem

Plants continuously produce organs throughout their life cycle due to the activity of the shoot apical meristem (SAM), which both initiates new lateral organs and maintains a population of stem cells. The SAM originates in the embryo although relatively little is known about the molecular events that precede and are required for its specification. Here, the authors use a combination of lasercapture microdissection and transcriptomic profiling both before and after SAM initiation (collecting both embryonic and seedling tissues) to identify genes that function during SAM initiation and are critical for SAM function. The authors were able to globally identify genes expressed at specific stages of SAM development, as well as in lateral organs. Interestingly, they found that genes required for lateral organ specification are expressed before genes that function instem cell maintenance, indicating that SAM organogenesis function is established before the stem cell maintenance function. This study also sheds light on the homology of specific organs including the scutellum and coleoptile, both of which appear to be leaf-like lateral organs based on gene expression patterns. In addition to providing key insights into the ontogeny of this critical structure, this study provides a wealth of molecular markers that can be used to dissect specific stages of SAM development and is a great resource for the community. Beth Thompson, 2012

9/2012 Addie Thompson
Hung, H-Y et al. 2012. Proc Natl Acad Sci, USA 159:1309-1318
   ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

The south-to-north spread of maize from its center of origin in southern Mexico required a significant adjustment in photoperiod sensitivity. While teosintes and tropical maize delay flowering under long days, temperate maize is less sensitive to day length. Here, Hung et al. investigate the genetic architecture of photoperiod sensitivity by measuring the difference in thermal time to flowering in long versus short day environments. Both the nested association mapping and diverse association mapping populations were utilized for mapping. A series of genome-wide association mapping and linkage mapping in subsequent populations allowed resolution of a QTL on chromosome 10 to ZmCCT, a gene homologous to rice Ghd7, a photoperiod response regulator. ZmCCT showed increased expression in alleles contributed by teosinte lines, leading to delayed flowering. This gene is thought to be one of a suite of genes that was under selection in postdomesticated maize by early humans to decrease photoperiod sensitivity, allowing for the northward spread of maize. This work provides insight into photoperiod sensitivity, its importance in postdomestication, and how it relates to previously mapped flowering time traits. In addition, the experimental approach outlines a thorough and complete investigation from large-scale genome-wide mapping down to the single gene level. Addie Thompson, 2012

9/2012 Beth Thompson
Dong, Z, et al. 2012. PLoS One. 7:e43450
   A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling

Regulation of flowering time is a complex process that involves both genetic and environmental inputs. The accurate prediction and genetic manipulation of flowering time has clear agricultural importance. Empirical models that predict flowering time exist, but these models are unable to make predictions for novel genotypes. The ideal model would incorporate both genetic and environmental factors to make accurate predictions. As a first step, the authors constructed a conceptual gene regulatory network that regulates flowering time in maize, synthesizing information on candidate genes and their relationships from work in maize, other grasses and Arabidopsis. To produce a quantitative, predictive model, they constructed a simplified dynamic gene network model, consisting of four key regulatory genes including the autonomous pathway members, ID1 and VGT1, and the integrators, DLF1 and ZMM4 (required to integrate inputs from multiple pathways that regulate flowering time). I will not (and admittedly cannot) comment on the mathematics, but the model successfully predicted zmm4 expression levels and total leaf number (as a proxy for days to tassel initiation) of novel genotypes. It will be interesting to see how the addition of new genes and environmental inputs impact the model and its predictions. While models that accurately predict flowering time are clearly important from an agricultural perspective, these models also play an important role in the discovery as they often make new (and unexpected) predictions and give experimental biologists new hypotheses to test. Beth Thompson, 2012

9/2012 David Braun
Kirienko, DR et al. 2012. Plant Physiol 159:1309-1318
   Reliable transient transformation of intact maize leaf cells for functional genomics and experimental study

Determining the subcellular localization of maize proteins via stable transformation is a relatively slow process. To circumvent the time required, transient expression assays are often employed. These approaches have some drawbacks, including heterologous expression systems, such as onion epidermis or Agrobacterium infiltration into a dicot leaf, or the isolation of maize protoplasts. An improved method for determining the cellular location for maize proteins in intact maize cells has been developed. Kirienko et al optimized particle bombardment transformation into developing maize adult leaves and identified the basal blade region close to the ligule as having the highest rates for transformation. The authors tested a constitutive strong promoter and terminator driving a cDNA-fluorescent protein translational fusion, and several genomic DNA constructs, with their endogenous regulatory sequences, exons, introns, and UTRs, fused to fluorescent proteins. Both types of constructs worked well in the assay. Cotransformation experiments, either both constructs being simultaneously transiently expressed, or transiently expressing one protein in a tissue already stably expressing a second fluorescent fusion protein, were successful. During these studies, no instances of mislocalization of the transiently expressed proteins were observed. The improved method of Kirienko et al will greatly expedite functional genomic and cell biological studies of maize proteins. David Braun, 2012

9/2012 Liza Conrad
Bolduc, N, et al. 2012. Genes Dev. 26:1685-1690
   Unraveling the KNOTTED1 regulatory network in maize meristems

The KNOTTED1 (KN1) homeodomain transcription factor functions to establish and maintain stem cells in plant meristems. This study combined expression analysis through RNAseq with chromatin immunoprecipitation (ChIP-seq) to identify genes regulated by KN1. Several thousand loci were shown to be bound by KN1, including both genes and a number of potential enhancer sequences. RNA-seq analysis focusing on only genes bound by KN1 revealed 643 genes that are bound and modulated by KN1, in other words, direct targets of KN1 regulation. These genes were enriched for transcription factors and hormone metabolism. Several transcription factor families known to be important in developmental programs such as homeobox, MADS, auxin response factors, (ARF), YABBY, and basic helix-loop-helix were identified. In addition to KN1 binding to auxin biosynthetic and transporter genes, it was also shown to bind to nearly half of the AUX-IAA and ARF genes in the maize genome. Thus, it appears KN1 regulates the auxin pathway at all levels. This comprehensive look at the KN1 regulatory network provides a solid foundation for broader studies on meristem function in plants. Liza Conrad, 2012

9/2012 Owen Hoekenga
Riedelsheimer, C, et al. 2012. Proc Natl Acad Sci, USA. 109:8872-8877
   Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

How do we sustain or even accelerate the pace of improvement that is so crucial for our bio-based economy? Genetics has carried us from pre-historical times (with plant domestication) into the historical (with plant improvement), and now leverages statistics and biology information in the present era (with biotechnology). As discussed previously, one of the new statistical approaches for plant improvement is genomic selection or whole genome prediction, which uses as many molecular genetic markers as available to enhance the accuracy of prediction models for agronomically important traits. However, genomic selection is a black box approach as no attempt is made to assign genetic markers to biological processes. Metabolomics can shine light into this black box, associating compounds and pathways of known or suspected biological significance with the genetic markers and agronomic traits. Adding genomics on top of metabolomics allows us to build both comprehensive explanations for complex traits, and also to create testable hypotheses to delve deeper into the mechanisms of plant growth and development. Here, a somewhat structured diversity panel was examined using metabolomic profiling. Previously, agronomic traits were correlated with particular metabolites (see April 2012 MEB). Now, due to the significant degree of linkage disequilibrium (r2 = 0.1 at 500 kb), metabolites were correlated with particular genomic regions. Twenty-six metabolites detected by mass spectrometry (including 17 unknowns) could be associated with SNPs at a particular significance threshold. As this diversity panel is genotyped at higher density or other varieties are included in this style of analysis, the number of associations between SNPs and metabolites will only go up and allow us to produce a far more complete understanding of the biochemical genetic bases of agronomically important traits. Owen Hoekenga, 2012

8/2012 Beth Thompson
Nelissen, H et al. 2012. Curr Microbiol 22:1183-1187
   A local maximum in gibberellin levels regulates maize leaf growth by spatial control of cell division

Plant organ growth and size is regulated by a combination of cell division and cell expansion. In the maize leaf, cell division and cell expansion occur in physically distinct regions. Cell division occurs at the base of the leaf in the division zone, while cell expansion occurs in the expansion zone, located adjacent to the division zone. The transition between the division zone and expansion zone is a major determinate of leaf growth. While plant hormones are known to be important regulators of plant growth, the mechanistic details of how the transition from cell division to expansion is still unclear. In this paper, Nelissen et al find that gibberellin (GA) has a key role in determining the boundary between the division and expansion zones and thereby regulating leaf growth. GA levels are highest at the boundary between the division and expansion zones and altering active GA levels shifts the position of the transition. In the leaf, high levels of GA are required to promote cell division in the distal portion of the division zone. This is in contrast to other plant tissues where GA primiraily promotes cell expansion, indicating hormones can have tissue-specific functions. Not surprisingly, the spatial regulation of GA levels is under tight control, and both GA biosynthesis and GA catabolism play important roles in restricting high GA levels to the division zone/expansion zone border. Beth Thompson, 2012

8/2012 Owen Hoekenga
Chia, J-M et al. 2012. Nature Genetics 44:803-807
   Maize HapMap2 identifies extant variation from a genome in flux

What do we mean when we talk about the maize genome? Are we referring to the genes, repetitive sequences and other hangers-on found in a single cultivar or speaking more broadly about many or all of the maize cultivars, landraces and other accessions at once? While there has been enormous value in the B73 genome, as per the Bermuda/Fort Lauderdale agreement sequence standards, as people look more widely using less expensive sequencing methodologies it is also clear that the maize genome has tremendous variability between accessions. This picture has become markedly clearer with the update of the maize haplotype mapping project (HapMap2), which now includes 103 inbreds, 23 landraces, 19 teosintes and a single accession of Tripsacum dactyloides, to serve as an out group. Applying independent bioinformatics pipelines identified segregating sites only 33% of the time from the same raw sequencing reads (13 billion reads amounting to ~1 trillion bp). 55 million SNPs were called at high confidence, with polymorphisms located to 21% of the gene models from the B73 reference genome. While nonsense mutations were far less abundant than synonymous or nonsynonymous substitutions, nearly 8% of genes in inbred maize had premature stop codons. Variation in sequencing depth for individual genes, as an estimate for copy number, indicated that 90% of sliding windows of 10 kb varied at least 2-fold among the study panel; variation in 70% of these sliding windows were found in greater than or equal to 10 accessions. Variation within the gene space of maize varieties is apparently larger than previously estimated, with potentially functional variation occurring at many loci. One of the next great challenges for current and future plant breeders and geneticists is therefore how to best capture and combine these functional variants to continue to enhance the performance of maize into the 21st century. Owen Hoekenga 2012

8/2012 Liza Conrad
Swanson-Wagner, R, et al. 2012. Proc Natl Acad Sci, USA. 109:11878-11883
   Reshaping of the maize transcriptome by domestication

In this study, expression profiling was performed on 38 maize and 24 teosinte genotypes to investigate how the maize transcriptome has changed through domestication. In addition to identifying more than 600 regions corresponding to genes that were most likely targets of selection during domestication, they also found five cases where selection may be acting on regulatory regions. Co-expression network analysis was used to reveal more than 1,100 genes with altered co-regulation during domestication regardless of whether their average expression changed for the individual genes. Furthermore, 45 genes were identified with altered expression in inbred maize relative to outcrossing teosinte. The majority of these genes have higher expression in maize and are enriched for involvement in chitin metabolism and defense response. This research goes beyond simply identifying genes selected during domestication and provides a more global picture of transcriptional changes due to: selection on regulatory regions, co-regulated gene networks, and changes in reproductive mechanism. Additionally, this in-depth transcriptome analysis adds more evidence to the impact that regulatory changes have on phenotypic diversity during evolution. Liza Conrad, 2012

8/2012 Addie Thompson
Li, X et al. 2012. Genome Res 22:2436-2444
   Genic and non-genic contributions to natural variation of quantitative traits in maize

The genetic control of plant morphology has long been investigated through the study of mutants displaying abnormal phenotypes. But what sorts of genetic changes lead to the natural levels of phenotypic variation observed in maize? With more sequencing data being released on an almost daily basis, many recent studies have focused on using large SNP datasets to associate genotypes with phenotypes. These studies lead to more questions: what proportion of phenotypic variation is controlled by changes in SNPs, and how are these SNPs distributed throughout the genome, including genic vs non-genic regions and distribution among promotors, introns, and exons? This paper attempts to answer these questions in an unbiased way using a collection of SNPs from the maize HapMap project, as well as an RNA-seq experiment on dissected shoot apices in the NAM founders that were then projected onto the RILs. Three leaf architecture and two flowering time traits were measured in the NAM population. A two-stage process was then used to identify SNPs associated with the traits. First, a low-resolution QTL mapping was conducted to identify rough regions of the genome using ~1100 tagging SNPs. Then the full set of 1.01 million SNPs was utilized in the target regions to identify specific SNPs associated with the trait. This approach was used instead of a whole-genome high-resolution scan in order to minimize false positives. The merits of the individual use of each SNP set in mapping are also presented and discussed. Although trait-associated SNPs were enriched for non-genic regions, these regions were most frequently within 5kb upstream of genes, and SNPs from the RNA-seq dataset frequently identified the genes implicated by HapMap SNPs. In addition, 79% of the explained variation (which was 44-59% of the total phenotypic variation) came from SNPs in genes or within 5kb upstream. In addition to suggesting increased efficiency in genic- and promoter-targeted GWAS experiments in other complex genomes, these results indicate that promoter regions, and thus gene expression regulation, are playing major roles in natural phenotypic variation. Addie Thompson, 2012

7/2012 David Braun
Weise, SE; et al. 2012. Plant Biotechnology Journal. 10:545-54
   Engineering starch accumulation by manipulation of phosphate metabolism of starch

Surplus carbohydrates assimilated during daylight can be transiently stored as starch in leaves. As opposed to kernel starch, phosphorylation of leaf starch is critical for proper metabolism. Transitory starch is phosphorylated by a glucan, water dikinase (GWD); mutations in this gene result in a starch excess (SEX) phenotype in Arabidopsis leaves. Weise et al identified a maize homolog of GWD and used RNAi to knock-down the gene's expression with the goal of increasing starch content in leaves. Starch levels in the leaves of RNAi plants were increased approximately 20-40-fold over controls, and starch accumulated to 15-26% of the dry weight of the leaves in the RNAi plants. The starch over-accumulating plants grew normally and accumulated above-ground biomass similar to the controls. As found in wild-type plants, even though the transgenic plants hyperaccumulated starch, the excess starch accumulated only in the bundle sheath cells. Plants engineered to contain high levels of modified leaf starch may be valuable for the production of biofuels, for silage, and for industrial applications. David Braun, 2012

7/2012 Liza Conrad
Barber, WT et al. 2012. Proc Natl Acad Sci, USA 109:10444-10449
   Repeat associated small RNAs vary among parents and following hybridization in maize

Small RNAs have previously been hypothesized to contribute to hybrid vigor or heterosis in plants. Using Illumina sequencing Barber et al. assessed the small RNA population in the seedling shoot apex and developing ear of two maize inbreds, B73 and Mo17 and their hybrid. Very few siRNAs were unique to a single or both parents or to the hybrid. Differences between parents and hybrids resulted from the hybrids inheriting distinct siRNAs from each parent rather than the generation of new siRNAs. These siRNA differences between the parental inbreds were enriched in 21- to 22-nt siRNAs from specific retrotransposon families. Furthermore, a reduction of 24-nt siRNAs by the mop1 mutation did not have an effect on the traits associated with heterosis. In conclusion, genetic variation in the regulation of transposable elements in the maize genome could contribute significantly to hybrid vigor. Liza Conrad, 2012

7/2012 Addie Thompson
Lin, Z et al. 2012. Nature Genetics 44:720-724
   Parallel domestication of the Shattering1 genes in cereals

This paper utilizes a variety of mapping techniques to identify the genes responsible for the evolution of the non-shattering seed phenotype in cereals. The gene, named Shattering1 (Sh1), was identified via mapping in sorghum as a YABBY transcription factor. Domesticated sorghum showed three haplotypes that each harbored a mutation that either lowered the expression or truncated the transcript of the gene, suggesting three separate origins of the non-shattering trait. Rice and maize orthologs of sorghum Sh1 were found to be located under shattering QTLs. An insertion in the rice ortholog caused decreased expression as well as a non-shattering phenotype. A whole-genome linkage analysis in maize showed strong narrow peaks over the two maize orthologs, which also contained insertions, structural changes, and frameshift mutations in domesticated maize inbreds relative to teosinte. This paper tells a tidy story of how different approaches to mapping can be combined with syntenic orthologous gene data across species to help link phenotype to genotype for an evolutionarily important trait. Addie Thompson, 2012

7/2012 Beth Thompson
Zhang, X et al. 2012. Plant Physiol 159:1453-1462
   PUNCTATE VASCULAR EXPRESSION1 (PVE1) is a novel maize gene required for leaf pattern formation that functions downstream of the ta-siARF pathway

Trans-acting siRNAs (ta-siRNAs) are a plant specific class of small RNAs that result from the intersection of the miRNA and siRNA pathways. miRNA-directed cleavage of a the non-coding TAS3 RNA is carried out by a specialized RISC complex, which contains AGO7, and generates ta-siRNAs that negatively regulate ARF3a. rgd2 contains a mutation in AGO7 and has severe developmental defects, including leaf growth and patterning. To identify genes that function downstream of rgd2/ago7 in leaf development, the authors isolated shoot apical meristems from rgd2 and normal plants using laser capture micro dissection, and looked from genes that were up or down regulated in rgd2 compared to normal. The authors identified a novel gene, PUNCTATE VASCULAR EXPRESSION1 (PVE1) that is significantly down regulated in rgd2/ago7 SAMs. PVE1 RNA is is expressed in developing vascular bundles and analysis of PVE1 mutants indicate that PVE1 is required for vascular development as well as leaf patterning. PVE1 promotes ta-siARF function and negatively regulates AGO1, and the authors propose that PVE1 functions in a distinct pathway that intersects and interacts with the ta-siARF pathway. Beth Thompson, 2012

7/2012 Owen Hoekenga
Hufford, MB, et al. 2012. Nature Genetics. 0:10.1038/ng.2309
   Comparative population genomics of maize domestication and improvement

What changes took place within the maize genome during domestication? The morphological changes regulated by loci such as teosinte branched1 (tb1) and teosinte glume architecture1 (tga1) are well known and easy to appreciate relative to the conversion of teosinte into recognizably modern maize. But what else happened to the genome at domestication and later, during improvement? This paper discusses the use of next-generation sequencing applied to 35 modern maize inbreds, 23 landrace accessions, and 17 accessions of wild relatives to an average depth of 5x coverage. It is now clear that domestication and improvement impacted allelic frequencies and local linkage disequilibrium at 1-2% of the gene space (recognized as the current filtered gene set). Some of the selective sweeps detected were larger in magnitude than those already detected at tb1 and tga1, but the effects of these changes are not immediately obvious to the form or function of the plant. Further, an appreciable fraction of the ~3000 locations in the genome that responded to domestication or selection are not obviously associated with the filtered gene set. This suggests, together with experimental evidence from gene expression profiling, that massive changes in cis regulatory sequences were also consequences to domestication and/or improvement, especially where there were not concomitant changes in the coding sequences. Together, these results indicate that allelic frequencies and identities have been altered at perhaps a far larger fraction of the genome than was previously appreciated. Future breeding efforts could concentrate at the re-introduction of allelic variation at these ~3000 loci to spur continued improvement of maize. Owen Hoekenga, 2012

6/2012 Owen Hoekenga
Lariepe, A et al. 2012. Genetics 190:795-811
   The genetic basis of heterosis: multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.)

One of the best tools developed to parse out the sources of genetic variance and to examine allelic effects in shared genetic backgrounds is the North Carolina Design III (NCIII) experiment. In this schema, members of a mapping population are backcrossed to both parents to create two derived but highly related mapping populations. Thus, homozygous and heterozygous allelic states can be compared in the two different genetic contexts of the two backcross populations. Lariepe et al (2012) have extended the NCIII design a step further, creating three recombinant inbred populations using parents from different heterotic groups. Instead of creating six derived populations from the three parental RI sets, nine populations were created using both backcrosses and a test cross to the unrelated parent. This expands on the power of the NCIII design to examine allelic effects in a third genetic context, which was used to address the bases for heterosis. The three prevailing theories for how heterosis is achieved are: dominance (that hybrids may have a larger number of effective genes than either parent); overdominance (that heterozygotes are superior to homozygotes at some loci); pseudo-overdominance (that genes of opposite effect are locked in repulsion to each other in low recombination regions of the genome). Epistatic interactions between loci are also thought by many to play large roles in heterosis. The augmented NCIII design allowed for powerful genetic dissection of several traits that are responsive to heterosis. Grain yield showed evidence of overdominance, while grain moisture showed evidence of additive effects (dominance) according to the QTL detected from data collected from multiple farm sites. Epistatic interactions were important for grain moisture, silking date and plant height but not grain yield. Pseudo-overdominance was also observed, as many QTL with opposite effects were located in centromeric regions. Owen Hoekenga, 2012

6/2012 David Braun
Liu, S; Yeh, C-T; Tang, HM; Nettleton, D; Schnable, P. 2012. PLoS One. 7:e36406
   Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

Bulk Segregant Analysis (BSA) is a method commonly utilized to map the genomic location of a mutant gene. RNA-Seq is a frequently employed approach to analyze gene expression between treatments or genotypes. Liu et al combined the two methods and developed Bulk Segregant RNA-Seq (BSR-Seq) to simultaneously map the genomic position of a mutant to a chromosomal locus and to analyze transcriptional changes between the mutant and wild-type populations. As a proof-of-concept, they mapped and cloned glossy3 (gl3), a gene controlling epicuticular waxes on juvenile leaves in maize. From a polymorphic segregating F2 population, RNA was independently isolated from a pool of 30 gl3 mutants and a pool of 30 wild-type siblings and analyzed by RNA-Seq. Bioinformatic analyses identified single nucleotide polymorphisms (SNPs) that distinguish alleles of expressed genes. These were mapped back to the B73 reference genome and used to look for enrichment of SNPs that clustered with the gl3 pool, narrowing the gl3 interval to ~2 Mb. By analyzing genes mapped in the interval whose expression differed between mutant and wild-type pools, a candidate gene was identified. Analysis of independently derived Mutator insertion alleles demonstrated that the correct gene was cloned. In addition to mapping and cloning a gene, the method has the added benefit of providing global expression data on changes resulting from the mutation. However, in order to clone the gene from the expression data, the causative mutation has to result in differences in transcript levels and must be expressed in the tissues collected for RNA isolation. Nonetheless, BSR-Seq will be a facile new approach to quickly map mutants in maize. David Braun, 2012

6/2012 Beth Thompson
Wingen, LU et al. 2012. Proc Natl Acad Sci, USA 109:7115-20
   Molecular genetic basis of pod corn (Tunicate maize)

Pod corn is a classical morphological mutant in maize, in which the glumes are enlarged and grow over the kernels. Based on this phenotype, pod cord was suggested to be an ancestral form of maize and has long been of significant interest to the maize community. Even though recent efforts to map genes involved in maize domestication have ruled out maize ancestor hypothesis, pod corn remains an intriguing mutant because of its striking phenotype. Pod corn is the result of a dominant mutation at the Tunicate (Tu) locus, which early genetic experiments suggested is complex. Until now the molecular basis of Tu locus has remained elusive. Here, Wingen et al provide evidence that the Tu locus is caused by a rearrangement of the promoter region and duplication of the ZMM19 gene. Interestingly, one ZMM19 duplicate has been inactivated in partial Tu revertants, and ZMM19 expression levels correlate with severity of the Tu phenotype. ZMM19 encodes a STMADS11-like MADS-box transcription factor. In contrast to most MADS-box TFs that function in floral development, ST-MADS11-like genes function in vegetative development. The authors show that ZMM19, which is normally not expressed in the inflorescence, is present in the inflorescence of Tu mutants. Furthermore, Tu mutant glumes exhibit more leaf-like traits and overexpression of ZMM19 in Arabidopsis transforms sepals into more leaf-like organs, suggesting that ZMM19 promotes development of leaf features. In addition to uncovering the molecular basis of a classic mutant, analysis of the Tu locus also illustrates the importance of gene copy number in regulating gene expression and morphological traits. Beth Thompson, 2012

6/2012 Liza Conrad
Zhang, Z et al. 2012. J Plant Physiol 169:797-806
   Characterization and expression analysis of six MADS-box genes in maize (Zea mays L.)

MADS-box transcription factors are essential regulators of a wide range of developmental processes including meristem and floral organ identity in plants. In this study, six MADS-box genes belonging to the SEP1/AGL2-like clade where characterized. Quantitative RT-PCR revealed 5 of the genes are highly expressed in silks, ears, seeds 5 DAP and tassels implying these genes may function in flower and fruit development. Yeast one hybrid results indicated that all six proteins are capable of functioning as transcriptional activators. One gene, ZMM7-L was further characterized to be nuclear localized and displayed expression changes in response to various abiotic stresses such as NaCl, PEG and ABA. The authors speculate ZMM7-L may be a negative transcription factor responsive to abiotic stress in maize. Liza Conrad, 2012

5/2012 Addie Thompson
Zerjal, T; et al. 2012. Theor Appl Genet. 124:1521-37
   Maize genetic diversity and association mapping using transposable element insertion polymorphisms

Transposable elements make up the majority of the maize genome, and active transposition can lead to changes in gene structure, number, and function. In this article, a small set of MITES were used as markers in 26 diverse inbreds, an association panel of 367 individuals, and a 322-member landrace panel. This allowed the researchers to investigate population structures, yielding results similar to those found using SSRs and RFLP markers. Genetic distance and geographic distance were found to be correlated, especially for landraces within 500km of each other. In addition, the association panel was utilized for association mapping using the MITE markers, where one rare tandem insertion was found to be linked to male flowering time. The insertion was found to be in a location not previously identified as associated with flowering time, close to a cytochrome P450 gene and in high LD with a mutation in the second exon. Several hypotheses for mechanisms of how the transposon itself might be interfering with gene expression are also discussed: the tandem insertions may form hairpin loops and restrict access to the gene, or the insertions themselves may contain siRNA sequences that serve as targets or producers of siRNA, altering gene expression. Studies like these provide insight into how transposable elements continue to alter the structure and regulation of the maize genome. Addie Thompson, 2012

5/2012 David Braun
Hiltpold, I et al. 2011. Plant Cell Environ 34:1267-75
   Systemic root signalling in a belowground, volatile-mediated tritrophic interaction

When leaf herbivores attack plants, plants release volatile organic compounds locally at the site of damage, and systemically from undamaged shoot tissues. The volatiles serve as chemical attractants to predatory insects of the herbivores. Thus, the plant, herbivore, and predator constitute a tritrophic ecological interaction, which has been well studied in shoots, but not investigated previously in roots. Hiltpold et al examined whether Western corn rootworm (WCR) could induce the production of volatiles from maize roots. They found that upon WCR feeding, (E)-b-caryophyllene (EbC) was induced locally at the wound site, and to a lesser extent, systemically in undamaged roots. Further, the authors showed that EbC functioned as a chemical attractant to an entomopathogenic nematode that is a parasite of WCR. Additionally, herbivory by WCR on maize roots induced the transcription of a gene that functions in the biosynthesis of EbC. Hence, root herbivory triggers the production of a volatile compound that attracts a predatory insect to help the plant defend itself. Perhaps as one way to mitigate the damage caused by WCR (estimated at more than $1 billion per year), corn breeders can select for plants with roots that produce greater amounts of EbC when attacked! David Braun, 2012

5/2012 Owen Hoekenga
Cook, J, et al. 2012. Plant Physiol. 158:824-34
   Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels

Enhancing sustainability and efficiency of 21st Century agriculture must be mindful of improving quality and yield for crops like maize. While grain yield has been a primary breeding target for many years, tailoring maize grain quality to better meet the needs of the food/feed industry, bioenergy concerns and ultimately the end users will also be very important. These stakeholders are aware of the competition between the carbon and nitrogen sinks of starch, protein and oils in the kernel. Fortunately, the genetic and environmental bases for these traits have been studied for a number of years. Recently, our understanding took a quantum leap forward with the use of the Nested Association Mapping and Inbred Association Panels to dissect these traits. Approximately twenty loci were identified for each trait, explaining 60% of the variance observed with largely additive effects based on seven locations worth of grain samples phenotyped by NIR spectroscopy. Allelic series were common, as 114-136 alleles were observed between starch, protein, and oil quality. Using the HapMap v1 SNP data, a causative gene underlying one of the oil QTL was identified. Given the decreasing cost of sequencing and our increasing knowledge of SNP diversity within maize, this phenotypic dataset will continue to be useful for many years to come as one can easily expect many more causative genes will be identified. Owen Hoekenga 2012

5/2012 Liza Conrad
Shen, Y; et al. 2012. PLoS One. 7:e32237
   Genome Expression Profile Analysis of the Immature Maize Embryo during Dedifferentiation

Genetic transformation of maize is a challenging process requiring the production of embryonic callus. The efficiency of inducing embryonic calli from immature embryo-derived cells is strongly genotype-dependent and varies greatly across maize inbred lines. Shen, et al. characterized the transcriptional changes that occur during three stages of dedifferentiation of maize immature embryos. 251, 324 and 313 differentially expressed genes where identified at stages I, II, and III of the maize inbred line 18-599R, respectively. Genes significantly changed during dedifferentiation were involved in amino acid and carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis and signal transduction mechanism. This study moves towards understanding the underlying mechanisms influencing embryo dedifferentiation with potential future implications in transformation efficiency in maize. Liza Conrad, 2012

5/2012 Beth Thompson
Studer, AJ; Doebley, JF. 2012. Genetics 191:951-958
   Evidence for a natural allelic series at the maize domestication locus teosinte branched1

Teosinte branched 1 (tb1) played a major role in the domestication of teosinte to maize and controls multiple developmental processes important for both plant architecture and ear morphology. Here, Studer and Doebley ask if tb1 also contributes to morphological variation in teosinte. To this end, the authors introgressed nine teosinte alleles into the W22 inbred background and measured 4 morphological traits known to be controlled by tb1 (including both ear morphology and plant architecture traits). They found three classes of teosinte tb1 introgressions: class I resembles maize in both ear morphology and plant architecture traits, class II produces teosinte-like plant architecture traits, but maize-like ear traits, and class III produce both teosinte-like ear morphology and plant architecture traits. Interestingly, these phenotypic classes correspond to the taxonomic origin of the alleles. There was no correlation between phenotype and the length of the introgressed chromosome segment, suggesting that tb1 and not a linked locus is responsible for the morphological variation. Although the authors were unable to identify the causal polymorphisms in tb1, they provide compelling evidence a natural allelic series that controls complex morphological traits in maize. Beth Thompson, 2012

4/2012 Liza Conrad
Gent, JI; Dong, Y; Jiang, JM; Dawe, RK. 2012. Nucl Acid Res. 40:1550-60
   Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation and H3 chromatin modifications

The domain adjacent to the centromere, the pericentromere, is essential for proper chromosome cohesion during cell division. Although the centromere is marked by a distinct histone variant, CENH3, there is no such defining characteristic known for the pericentromeric region. In this study, genome-wide sequencing laid the foundation to compare RNA expression levels, DNA methylation and histone modification between the centromere, pericentromere and the chromosome arms. Surprisingly, this thorough epigenetic profiling revealed very little difference between pericentromeres and centromeres. Rather, it showed that pericentromeres are an intermediate state between centromeres and the chromosome arms with respect to siRNAs, DNA methylation, poly(A)-enriched RNA and four Histone3 modifications. The authors conclude that the two primary properties of the pericentromere, chromosome cohesion and suppressed recombination rates, may result from indirect affects of kinetochore binding and its proximity to the centromere rather than an epigenetic state distinct to the pericentromere. Liza Conrad, 2012

4/2012 Owen Hoekenga
Riedelsheimer, C, et al. 2012. Nature Genetics. 44:217-20
   Genomic and metabolic prediction of complex heterotic traits in hybrid maize

The term genetical genomics was coined a number of years ago to express the combination of traditional genetic analyses with systems biology approaches such as transcriptomic analysis. Common genetical genomics experiments examine quantitative trait loci that regulate patterns of gene expression or other similar hybrids of old and new. In a similar vein, genetical metabolomics integrates a combination of approaches to dissect the bases of traits of interest using small molecule profiling. Investigators used a tried-and-true approach of evaluating performance of a large test cross panel (285 diverse inbred Dent lines with two different testers), looking for correlates for yield components such as dry matter, plant height and starch content. What sets this work apart is the use of whole genome prediction (sometimes also called genomic selection), where all available genetic marker data are used to create a statistical model to explain and predict the trait(s) of interest. Here, marker information was obtained using a 56K SNP chip to genotype the study panel. Further, authors expanded beyond the simple biochemical traits of sugar, starch and lignin content to using gas chromatography/mass spectrometry to phenotype the metabolome in leaves 33 days after sowing. This snapshot of metabolism and plant performance was included in the whole genome prediction models to help explain plant performance at maturity. If a leaf metabolome from young plants could be useful to predict final dry weight or other yield components, this could represent a significant savings in time and effort and allow more rapid selection of improved germplasm within a breeding context. The authors found that for some traits, the leaf metabolome did nearly as good a job as the genome wide SNP data set for predicting outcomes such as female flowering time, dry matter concentration and starch content. SNPs did better at predicting at lignin content, dry matter yield and plant height. However, it is worth noting that only 130 metabolites were phenotyped (a 400-fold difference in scale) such that genetical metabolomics represents a powerful new approach for plant improvement. Owen Hoekenga, 2012

4/2012 Addie Thompson
Davidson, RM et al. 2012. Plant J 71:492-502
   Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution

Though not about maize specifically, this article utilizes comparative transcriptome sequencing in multiple tissues of three closely related species from three subgroups of the Poaceae family of grasses: brachypodium, rice, and sorghum. The analysis first focused on the genes in common across the species, identifying a set of around 13,000 common genes. Co-expression networks were investigated, and it was found that of the shared genes, expression was more similar in conserved tissues like anthers and leaves than in reproductive tissues such as seeds and flowers. Interestingly, more shared genes contribute to lineage-specific reproductive expression than lineage-specific genes. The article also investigates regulatory evolution as related to expression levels and gene function, finding that genes with high expression levels are GO-term enriched for housekeeping, and selectively constrained. A shared whole genome duplication event prior to speciation also allows for exploration of the diversification of homologous gene pairs within and among species, with orthologous gene pairs in blocks of genomic colinearity between species showing increased conservation of expression. Many of these concepts have been or are starting to be investigated in maize, and having additional datasets from related species will allow further study into evolutionary implications of genome-wide transcription variation. Addie Thompson, 2012

4/2012 Beth Thompson
Hansey, C, et al. 2012. PLoS One. 7:e33071
   Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

In this work, the authors used RNA-sequencing to define the transcriptome of seedling tissue from 21 diverse maize inbred from the two major heterotic groups (stiff stalk and non-stiff stalk germplasm). Through this work, they were able to identify a core genome, which includes genes expressed in all the inbreds sampled (50% of all genes) and a dispensable genome, which includes genes that are only expressed in one or a subset of the inbreds sampled (28% of all genes). The dispensable genome is likely be a major contributor to the great phenotypic diversity observed in maize. In addition, the authors identified an additional 351,710 SNPS from genic regions (in 22,830) genes. Because these SNPs are present in genic regions, they have the potential to alter protein function. The authors also identified an additional 1300 novel transcripts, including most of which are likely not present in the B73 genome. Interestingly, 150 of the novel transcripts are only present in one heterotic group, giving support to the attractive hypothesis that presence/absence variation could be a major contributor to heterosis. Beth Thompson, 2012

4/2012 David Braun
Barbaglia, AM, et al. 2012. Genetics. 190:965-75
   Gene capture by helitron transposons reshuffles the transcriptome of maize

Helitrons are an unusual class of transposable elements that have the propensity to capture fragments of genes and transpose them to new locations in the genome. Some of these gene fragments are transcribed and detected as ESTs. Barbaglia et al., computationally analyzed the B73 genome sequence for Helitrons and made several interesting discoveries: Helitrons compose almost 1% of the B73 genome, many Helitrons show plus/minus variation of being present in the B73 genome, but not in the Mo17 genome, some Helitron-derived ESTs show alternative spliced forms between root and shoot tissues, and in at least one case, an exon outside of a Helitron insertion was joined to the Helitron-derived transcript. These data show that gene fragments captured by Helitrons, as well as flanking exons, can be expressed as chimeric transcripts and may lead to the evolution of new genes. David Braun, 2012

3/2012 Beth Thompson
Fouquet, R et al. 2011. Plant Cell 23:4280-4297
   Maize rough endosperm3 encodes an RNA splicing factor required for endosperm cell differentiation and has a nonautonomous effect on embryo development

The endosperm is critical to support normal embryo growth and development and is a key determinate of seed size. While we know that the developmental programs of the embryo and endosperm must be carefully integrated, we know relatively little about the signaling that occurs between these two tissues. Here, the authors employed a clever strategy using B-A translocations to find seed mutants with nonautonomous roles in the endosperm and embryo. This work focuses on Rough Endosperm3 (Rgh3), which functions in the endosperm to promote embryo development. Specifically, they found that Rgh3 is required to promote the switch from cell proliferation to differentiation in the endosperm. This observation suggests that endosperm viability per se is not sufficient to promote embryo development, but rather at least one specific endosperm cell type is required to promote normal embryo development. Rgh3 encodes the RNA splicing factor U2AF35, a core splicing factor. Splicing is not globally perturbed in rgh3 mutants, rather splicing defects are limited to a subset of alternatively spliced mRNAs. Analysis of these aberrantly spliced transcripts (and investigation of the normal function of these genes) provides a potential inroad to identify endosperm-embryo signaling molecules and the endosperm cell types that are essential for this signaling. Beth Thompson, 2012

3/2012 Owen Hoekenga
Gaudin, AC; McClymont, SA; Raizada, M. 2011. Crop Sci. 51:2780-2795
   The Nitrogen Adaptation Strategy of the Wild Teosinte Ancestor of Modern Maize, Zea mays subsp. parviglumis

While the impact of domestication on the form and function of the maize plant has been considered for many years, the majority of attention has been placed above ground. Roots are not an easy system to study and have largely been ignored. An innovative aeroponics apparatus has been designed to allow plants to be grown to maturity using controlled nutrient environments and to have their roots systems easily visualized and sampled for additional study. This aeroponic approach allowed quantitative traits of root architecture, reporter gene expression and nitrogen use efficiency to be examined in teosinte and the W22 inbred. Teosinte and other wild plants are well adapted to irregular soil environments, making more out of less. Modern maize inbreds have been optimized to grow in uniform and nutrient-dense soil environments. However, with increasing fertilizer costs and a wish to decrease the impact of agriculture on the broader environment, having a better understanding of how wild relatives adapt to low nutrient environments has high value. This study establishes a procedure for collecting accurate and reproducible trait data to guide these future efforts in understanding the molecular genetic, physiological, and developmental underpinnings of nitrogen use efficiency. This information will be extremely useful to enhance the sustainability of agriculture. Owen Hoekenga, 2012

3/2012 Addie Thompson
Whipple, C et al. 2011. Proc Natl Acad Sci, USA 108:E506-E512
   grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses.

One of the major domestication genes in maize, teosinte branched1 (tb1), plays a role in suppressing tiller development and lateral branching. Whipple et al. describe the cloning and characterization of grassy tillers1 (gt1), a class I homeodomain leucine zipper gene that significantly reduces tillering and lateral branching. Both gt1 and tb1 show evidence of selection in domestication, and map to tillering and branching quantitative trait loci. Expression of gt1 is dependent on tb1, and is regulated by light in sorghum and teosinte. These results indicate that gt1 acts in the shade avoidance response pathway to reduce tillering and lateral branching, contributing to domestication traits and plant architecture in modern maize. Regulation of shade avoidance and tiller growth have have both been implicated in the modification of important agronomic traits such as increased biomass and yield in other grasses, making characterization of genes in these pathways potentially useful to crop improvement. Addie Thompson, 2012

2/2012 Liza Conrad
Costa, LM, et al. 2012. Curr Biol. 22:160-5
   Maternal control of nutrient allocation in plant seeds by genomic imprinting

In plants, parent-of-origin specific gene expression, also known as imprinting, occurs primarily in the endosperm. The main function of the endosperm, similarly to the placenta of mammals, is to provide nourishment to the growing embryo. In the mammalian placenta, imprinted genes regulate the flow of nutrients from mother to fetus. This analysis of the Maternally expressed gene1 (Meg1) is the first report of any imprinted plant gene functioning in maternal nutrient allocation to the embryo. This study establishes that Meg1 is required for transfer cell differentiation, sugar homeostasis and nutrient partitioning during seed development in maize. Precise temporospatial expression of Meg1 promotes differentiation of the endosperm transfer tissue in the developing endosperm. The authors clearly demonstrate that Meg1 functions in a dosage dependent manner that is regulated through imprinting. Consequently, the loss of imprinting or increase in dosage results in an increased distribution of maternal resources into the endosperm having effects on seed size and sugar partitioning. Liza Conrad, 2012

2/2012 Owen Hoekenga
Yan, J et al. 2010. Nature Genetics 42:322-327
   Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain

Vitamin A deficiency is a serious, worldwide health problem. Increasing the concentration of Vitamin A-precursor carotenes in cereal grain is one way to address this crisis. A previous study identified variation at the maize lycopene epsilon-cyclase (LYC-E) gene as associated with beta-carotene concentration in maize kernels. LCY-E function is necessary for flux down the alpha-carotene branch of the carotenoid pathway; LCY-E alleles favorable for beta-carotene accumulation show reduced expression and increased flux down the beta-carotene branch. In this study, variants at a second gene in the carotenoid biosynthetic pathway, beta-carotene hydroxylase 1 (crtRB1), are also associated with beta-carotene concentrations in maize grain. crtRB1 carries out both the hydroxylation of beta-carotene to beta-cryptoxanthin, which has only half the provitamin A activity, and its further hydroxylation to zeaxanthin, which has no provitamin A activity. Interestingly, crtRB1 alleles associated with increased beta-carotene content fall into two classes: those showing reduced expression, and those showing reduced enzymatic activity. Some crtRB1 alleles appear capable of hydroxylating beta-carotene only once, to produce beta-cryptoxanthin, and not a second time to produce zeaxanthin. The "best" crtRB1 allele is very effective at hydroxylating beta-carotene all the way to zeaxanthin, but shows very low expression in endosperm. Since the carotenoid pathway carries out other essential functions, it is preferable to select variants with tissue-specific expression differences rather than variants with altered enzymatic activity. The LYC-E and crtRB1 alleles most favorable for beta-carotene accumulation (found in tropical and temperate germplasm, respectively) are now being combined for the first time. Pat Brown, 2010

The World Health Organization considers iron, iodine and vitamin A deficiencies to be the most prevalent and severe micronutrient limitations to human health around the world. Iodine can easily be added to irrigation water or table salt to reduce the incidence of iodine deficiency. Biofortification of crops with iron is in its infancy, but shows promise. Biofortification of crops for vitamin A, on the other hand, is a clear demonstration of the power and promise of genomics-assisted breeding. Comprehensive knowledge of the biochemical genetics for the synthesis of beta-carotene and other carotenoids from Arabidopsis thaliana enabled candidate gene-based association mapping in maize. This identified the key bottlenecks for increasing those carotenoids that can be converted by people into vitamin A, which includes beta-carotene and beta-cryptoxanthin. The association mapping results were validated using linkage mapping, confirming that polymorphisms at beta-carotene hydroxylase1 (crtRB1) were responsible for variation in beta-carotene levels. As it happens, alleles that occur at low frequency in a subset of germplasm pools were responsible for the desirable outcome. Gene expression studies clarified that lack of crtRB1 gene expression was correlated with increased levels of beta-carotene. Variation at this single locus transformed maize grain from a negligible to substantial source of pro-vitamin A, meeting nearly 45% of the breeding target of 15 μg/g. Combining the useful alleles at crtRB1 and a second key regulator, lyce1, suggest that the breeding target can be easily met. However, as the best combination of alleles to biofortify maize grain with pro-vitamin A carotenoids are found in geographically and genetically distinct germplasm pools, it is unlikely that the full potential would have been realized without this genomics-based approach. Owen Hoekenga, 2012.

2/2012 Addie Thompson
Waters, Amanda J., et al. 2011. Plant Cell. 23:4221-33
   Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm

Imprinting, or expression dependent upon the parent of origin, is an important mechanism in the regulation and development of the triploid plant endosperm. Here, Waters et al. investigated imprinting of endosperm and embryo tissues 14 days after pollination using RNA sequencing. By comparing allele dosage of expressed genes with parental sequence polymophisms, they identified 100 putatively-imprinted genes in the endosperm. About half of these imprinted genes were found to be preferentially expressed in the endosperm relative to other tissues. Since DNA methylation and chromatin changes are thought to play a role in imprinting, methylation in the tissues was also investigated. Hypomethylation of the maternal allele in the endosperm was observed in all cases tested. Putative imprinted genes were compared to those previously identified in rice and Arabidopsis, identifying 10 imprinted genes conserved among species. Addie Thompson, 2012

2/2012 David Braun
Wahl, R; Wippel, , K; Goos, S; Kamper, J; Sauer, N. 2010. PLoS Biol. 8:e1000303
   A novel high-affinity sucrose transporter is required for virulence of the plant pathogen Ustilago maydis

Corn smut, Ustilago maydis, is an important pathogen of maize. As a biotrophic fungus, U. maydis obtains carbohydrate resources from its host plant. To do so, U. maydis hyphae form contact zones with the plasma membrane of infected host cells. Uptake of extracellular sucrose from the cell wall (apoplast) allows growth of the fungus and results in tumor formation on the infected plant organ. Wahl et al. identify a protein, Srt1, from U. maydis distantly related to plant sucrose transporters (SUTs), which transport sucrose from the apoplast into the cytoplasm. The authors show that deletion of Srt1 reduces the virulence of the fungus. Additionally, they demonstrate that Srt1 localizes to the fungal plasma membrane, is induced by sucrose in developing tumor tissue, and has a higher affinity for sucrose than previously characterized plant SUTs. These data indicate that the fungus can outcompete the host for apoplastically localized sucrose. Furthermore, by using Srt1 to import sucrose directly, rather than cleaving it into hexoses via cell wall-bound invertases, the fungus avoids triggering the host hexose-induced defense responses. Hence, Srt1 functions to provide sucrose to the fungus, and it provides a mechanism to bypass production of signaling molecules that initiate plant defense responses. David Braun, 2012

1/2012 David Braun
Studer, A; Zhao, Q; Ross-Ibarra, J; Doebley, JF. 2011. Nature Genetics. 43:1160-1163
   Identification of a functional transposon insertion in the maize domestication gene tb1

Maize was domesticated from its wild relative teosinte. One of the key domestication traits between maize and teosinte was a change in plant architecture, which is controlled by the teosinte branched1 (tb1) locus. Previous work had shown that changes in expression levels of tb1 in maize correlate with alterations in branching. Additionally, the sequences controlling the expression changes were mapped to the upstream regulatory region of tb1. In the current paper, the authors map polymorphisms between maize and teosinte in the tb1 promoter and identify a Hopscotch retrotransposable element insertion into the maize sequence. Promoter:reporter expression assays in maize leaf protoplasts show that the Hopscotch element causes a two-fold increase in expression, which is similar to the differences in tb1 expression assayed between maize and teosinte. Interestingly, the authors determined that the Hopscotch insertion predated domestication, demonstrating that the tb1 allele selected by early maize farmers was already present in teosinte. Hence, this work is an elegant illustration of the power of transposons to cause variation and the evolution of genetic novelty. David Braun, 2012

1/2012 Liza Conrad
Eichten, S et al. 2011. PLoS Genet 7:e1002372
   Heritable Epigenetic Variation among Maize Inbreds

This study examined the whole genome CG methylation patterns in two different maize inbreds allowing the authors to tease apart genetic from purely epigenetic variation. A total of nearly 700 Differentially Methylated Regions (DMRs) were identified in B73 and Mo17 with a subset of these DMRs occurring in identical-by-decent regions were little or no sequence variation is present. Overall, the authors discovered that the majority of the DMRs occur in intergenic regions however a small number of DMRs do overlap with genes. Genes found within the DMRs are generally hypomethylated, high-confidence genes with higher expression levels, and are in syntenic positions relative to other grasses. Interestingly, there was no detectable difference in methylation between maize subgenome1 and subgenome2 from Schnable, et al 2011 even though subgenome1 is more highly expressed. The use of near-isogenic lines allowed the authors to evaluate the inheritance and whether the methylation in these DMRs is controlled by genetic differences elsewhere in the genome. The majority of DMRs (85%) were stably inherited. Furthermore, a small subset (3/13) of the stably inherited DMRs show evidence of trans-acting control of the DNA methylation. This study demonstrates the presence of purely epigenetic variation and provides a foundation for further research into the phenotypic effects of epigenetic variation in maize. Liza Conrad, 2012.

1/2012 Owen Hoekenga
Lung'aho, MG, et al. 2011. PLoS One. 6:e20429
   Genetic and physiological analysis of iron biofortification in maize kernels

Some have joked that the three most important breeding targets of the last several decades have been yield, yield, and yield. The success of the hybrid seed industry and the gains made by the Green Revolution both speak to the importance of yield in a breeding program. However, the fraction of the world's population that do not have their nutritional needs met by cereal staple-centered diets suggest that a Second Green Revolution must add nutritional quality to the target list. Iron should be on that list as ~2 billion people around the world have iron deficiency or anemia, largely due to inadequate diets brought on by poverty. Iron nutritional quality is a combination of iron concentration and bioavailability, the fraction that is easily absorbed and utilized by the consumer. Unfortunately, the fraction of bioavailable iron in cereals is small (<10%) and the genetic and chemical bases for this trait are just beginning to be understood. The authors used a human cell culture based bioassay to phenotype iron bioavailability in the IBM RI set per se, without preconceptions as to the potential causes. Iron bioavailability was not well correlated with either iron or phytic acid concentration, suggesting that novel factors were at work. More, larger QTL were detected for iron bioavailability than iron concentration, suggesting that while more difficult to phenotype that iron bioavailability may have a simpler genetic basis than iron concentration. NILs evaluated at five sites outside of the author's home site indicated efficacy beyond central New York. This report marks an important first step towards the biofortification of maize with iron. Owen Hoekenga, 2012

1/2012 Beth Thompson
Hartwig, T et al. 2011. Proc Natl Acad Sci, USA 108:19814-19819
   Brassinosteroid control of sex determination in maize

This paper adds brassinosteroids (BR) to the growing list of hormones that function in maize sex determination. Previous work has shown that BRs have roles in cell elongation, photomorphogenesis and vascular differentiations, however their roles in sex determination have been speculative. Here, the authors report the characterization and cloning the classical mutant, nana plant1 (na1). na1 exhibits a dwarf phenotype characteristic of BR mutant, as well as feminized tassel florets (the tasselseed phenotype), resulting from lack of pistil abortion in the tassel. The authors found that na1 encodes a DET2 homolog, a key enzyme in the BR biosynthetic pathway. BR levels are reduced in na1 mutants and BR inhibitors phenocopy na1 mutants, confirming the role of BR in maize sex determination. na1 is expressed in anthers throughout anther development, suggesting that local BR synthesis might promote stamen maturation in tassels. Interestingly, BR are steroid-like hormones, illustrating the key roles steroid hormones play in both animals and plants. Beth Thompson, 2012

1/2012 Addie Thompson
Brown, PJ, et al. 2011. PLoS Genet. 7:e1002383
   Distinct genetic architectures for male and female inflorescence traits of maize

Maize morphology, particularly that of the reproductive organs, has changed dramatically throughout the process of domestication and subsequent directional selection. This shift in plant architecture was brought about by changes in genetic architecture. This paper investigates the genetic architecture of ear and tassel morphology as compared to that of previously studied flowering and leaf traits. Unlike previous investigations in the NAM population where traits were found to be predominantly controlled by many loci with very small effects, inflorescence traits displayed a shift in genetic architecture toward increased effect sizes, particularly for ear morphology. It is suggested that the larger effect sizes observed in the ear are the result of cryptic variation released after domestication mutations became fixed, leading to instability of ear traits and allowing strong directional selection to occur and be maintained over time. The paper also discusses pleiotropy among the traits, and investigates the proximity of QTL to known inflorescence-implicated mutants and domains. Addie Thompson, 2012

12/2011 Michael Muszynski
Schaeffer (Polacco), ML, et al. 2011. Database (Oxford). 2011:bar022
   MaizeGDB: curation and outreach go hand-in-hand

It seems particularly fitting to end my year on the MEB with a paper celebrating the 20th anniversary of the MaizeGDB. This article provides a brief historical overview of the MaizeGDB and how it has evolved into the essential community resource it is today. Although initially focused on maps, markers and literature, today the MaizeGDB primarily focuses on the integration of reference genome sequences and sequence-based expression datasets through user-friendly query interfaces and data displays. The centerpiece to this effort is the MaizeGDB Genome Browser which hosts tracks for genome annotation from genome projects (e.g., PlantGDB, and sequence-indexed tracks from individual community research projects. As a roadmap to ensure future success and significance, this article outlines several ways the maize research community can collaborate with MaizeGDB. The longevity of the cooperative nature of our community is illustrated by a picture in this article of two meetings at Allerton, IL, separated by a mere 48 years. Mike Muszynski, 2011

12/2011 Aaron Lorenz
Zhao, Y et al. 2011. Theor Appl Genet 124:769-776
   Accuracy of genomic selection in European maize elite breeding populations

Genomic selection is a marker-based selection method that strives to maximize prediction accuracy for highly complex traits, such as grain yield. High marker densities available now at reasonable costs allow the development marker-based prediction models that are potentially useful across biparental breeding populations. Zhao et al. used real yield data gathered at 10 Italian locations to empirically evaluate genomic selection. They found that marker-based prediction accuracy for yield was approximately equivalent to the prediction accuracy of phenotypes consisting of means across three to four environments with one rep. The cost of genotyping is about the same as the cost of phenotyping at this level, but genotyping and genomic selection can be performed year round. The most interesting thing I found about this paper was that data from different, but highly related breeding populations, did not boost the prediction accuracy within populations despite a six-fold higher population size for effect estimation. This could be caused by 1) epistasis, 2) different QTL alleles segregating across populations, and 3) different QTL-marker linkage phases across populations. More work is needed to leverage data from across an entire breeding program to maximize the prediction accuracy within individual bi-parental breeding populations. Aaron Lorenz, 2011

12/2011 R. Keith Slotkin
Roudier F. et al., 2011. EMBO J. 30:1928-38
   Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

There are dizzying arrays of post-transcriptional histone modifications that can influence the regulation of a gene. These histone modifications often do not work independently, but rather occur in a limited number of specific combinations. Roudier et al produced epigenomic maps of eight histone modifications in Arabidopsis, and combined these with analysis of three additional previously performed histone modifications and DNA methylation. From this analysis, four main plant chromatin types were elucidated. These four chromatin states are: Actively transcribing genes, developmental stage-specific polycomb-regulated genes, heterochromatin-associated epigenetically silenced transposable elements, and a category of genomic regions not associated with any specific chromatin mark. It will be interesting to determine if all maize chromatin can be categorized into one of these four chromatin states, or if the increased size and complexity of the maize genome will translate into additional major classes of chromatin states. R. Keith Slotkin 2011.

12/2011 Clinton Whipple
Djamei, A. et al., 2011. Nature. 478:395-8
   Metabolic priming by a secreted fungal effector

Usitlago maydis is a well-known fungus known causing corn smut. Maize plants infected with U. maydis undergo dramatic developmental alterations induced by the fungal parasite resulting in large tumors. Infection begins when a fungal hyphae injects effector proteins into the plant cell that promote virulence by suppressing the natural defenses of the plant. This paper demonstrates that U. maydis employs a chorismate mutase as an effector protein. Chorismate is a metabolite produced by shikimic acid pathway that can act as a precursor in the production of essential aromatic amino acids (prephenate pathway), or alternatively is used in other pathways including the production of salicylic acid. Chorismate mutase takes chorismate down the prephenate pathway. Upon injection of the fungal chorismate mutase it is able to move, presumably via plasmodesmata, to neighboring cells and prime the host cellular metabolism to favor the prephenate pathway and as a result compromise the production of the defense hormone salicylic acid. The authors note that many plant parasites express chorismate mutase, suggesting that this may be a common mechanism to promote virulence. Clinton Whipple, 2011

12/2011 Paul Scott
Kump, KL et al. 2011. Nature Genetics 43:163-8
   Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

NAM strikes again! Nested association mapping is a method for identifying genes that control traits. It has been used previously to dissect flowering time and in this publication it was applied to resistance to the maize pathogen southern leaf blight (SLB). The key to NAM is a set of nearly 5000 recombinant inbred lines derived from 25 diverse inbred lines crossed to B73 to form families of F2-derived lines. The authors scored these lines for resistance to SLB and identified 32 significant QTL. Thanks to the availability of high resolution genotypes for the NAM population, it was also possible to carry out genome wide association tests at 1.6 million polymorphisms. This analysis led to the identification of 245 significant polymorphisms. The authors then combined the QTL and genome-wide association results by developing a model to explain the phenotypic variance. This model contained terms from both analyses. QTLs were replaced by SNPs where possible to achieve the highest possible resolution. The final model explained 74% of the variation for SLB resistance and contained 51 single nucleotide polymorphisms and three QTL. Many of the genes identified in this study have functions related to plant defense and/or map to positions of QTL identified in other studies. While this is a satisfying result, it is not surprising because most of the previous studies involved populations derived from B73 and some were subsets of NAM. The genes identified in this study are attractive targets for studies of disease resistance at the molecular level. It will be interesting to see how these results are translated into breeding strategies. Paul Scott, 2011

11/2011 Paul Scott
Bousios, A et al. 2012. Plant J 69:475-488
   The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story

The maize genome has been described as a series of gene-rich islands floating in a sea of retrotransposons. This paper is about the sea. About three quarters of the maize genome is made up of LTR retrotransposons. In maize, copia is one of the largest families of LTR retrotransposons. The authors of this paper exploit a new method of identifying one type of copia elements, the sireviruses, to examine the relationship among copia family members in maize. Their approach reveals new relationships and allows classification of many previously unclassified elements. These results clarify how this family of retrotranposons evolved and suggests that the sireviruses are the only copia family members to successfully proliferate in maize. Even dedicated island dwellers will appreciate this well-written and illustrated paper about the maize genomic sea. Paul Scott, 2011