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12/2017 Ruben Rellan-Alvarez
Wang, L, et al. 2017. Genome Biol. 18:215
   The interplay of demography and selection during maize domestication and expansion

After domestication in the Balsas River Basin the current state of Guerrero in Mexico, maize colonized a variety of different environments with very different conditions than its original humid, subtropical habitat. While the evolutionary and genetic processes that occurred during maize domestication have been studied in detail, local adaptation of maize to new environments have received much less attention. In this paper, Li Wang and collaborators studied how demographic history and selection shaped maize diversity during maize spread across the Americas. The authors found that maize experienced severe declines in effective population size due to domestication bottlenecks and serial founder effects, the latter, is particularly significant in Andean landraces. On the other hand, the wild relative teosinte parviglumis experienced population growth. This has led to a higher number of deleterious alleles in maize when compared with teosinte. Introgression from another teosinte (teosinte mexicana) that is prevalent in highland Mexico reduced the effect of deleterious alleles in the maize populations like highland Mexico, Guatemala and South West US where maize was able to hybridize with this highland teosinte. This study highlights the opportunity to explore teosinte genetic diversity to incorporate beneficial alleles into modern maize breeding pools and provides a foundational study to understand the evolutionary processes that allowed maize to colonize and be cultivated all around the globe. Ruben Rellan, 2017




12/2017 Fang Bai
He, Y, et al. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1713225114
   Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize

Meiotic recombination is a key reason for the genome stability and genetic variation in plants and animals. Meiotic recombination is beginning with the forming double-strand breaks (DSBs). Maize has a 2500 Mbp genome and a large distribution of transposons and repetitive sequences. In this paper, He et al. Mapped meiotic DSBs hotspots to the maize reference genome by using the chromatin immunoprecipitation (ChIP) combined with the sequencing of the segments on the Illumina platform. They found that DSB hotspots were around 1.2 kb long and spreaded on the maize genome randomly with the majority of DSB hotspots were located in repetitive DNA, primarily Gypsy retrotransposons. Furthermore, the authors conducted micrococcal nuclease digestion of chromatin and immunocolocalization of H3K4me3 marks and RAD51 foci in a maize meiocyte at zygotene to search for factors controlling DSB locations. They found that DSBs are formed at nucleosome-free and DNA-hypomethylated sites in maize. In addition, He et al. identified a 20-bp-long GC-rich degenerate DNA sequence motif in about 72% of genic DSB hotspots, but not in the repetitive DNA hotspots. The authors also investigated the relationship between the DSB distributions with the chromosomal cross overs (CO) distributions based on the recombination data from the maize Nested Association Mapping. Fang Bai, 2017




12/2017 Jason Wallace
Gage, JL, et al. 2017. Nature Communications 8:1348
   The effect of artificial selection on phenotypic plasticity in maize

Phenotypic plasticity refers to how an organism can adjust its growth based on its environment. In agriculture, this most often manifests as gene-by-environment interaction (GxE). Plasticity / GxE can complicate crop breeding because performance in one environment does not necessarily predict performance in another, although breeders can also exploit it to create lines well suited to particular environments. Gage et al. investigated phenotypic plasticity in the maize Genomes to Fields dataset to determine if modern breeding has selected for or against phenotypic plasticity. They found that regions of the genome that were selected for temperate grain production show less contribution to GxE for yield, indicating that modern breeding has selected against plasticity in favor of yield stability across environments. A similar analysis of height showed no such selection. Genetic regions associated with plasticity were also enriched in the 5 kb upstream of genes, implying that regulatory variation has an outsize contribution to phenotypic plasticity and GxE. Jason Wallace, 2017




12/2017 Lin Li
Ma, SS; Ding, ZH; Li, PH. 2017. BMC Plant Biology. 17:131
   Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response

Co-expression networks have been evidenced to harbor the patterns of transcriptome organization and suggest common biological functions for networked genes. With the advent of Next generation sequencing, tons of transcriptome data have been accumulated, which provides us an unprecedented chance to construct comprehensive co-expression networks for the dissection of gene functions and regulatory relationships. Ma and colleagues have collected a massive RNA-Seq data and constructed a comprehensive co-expression network with 964 gene modules for 20269 genes. These modules are likely to be involved in a series of biological processes. Interestingly, comparative co-expression network analysis illustrated the conservation and divergence of biological pathways between species. This study provides a sound genomic resources potentially for the future functional studies in maize. Lin Li, 2017

Data Can be found here: http://staff.ustc.edu.cn/~sma/maizeggm.html




11/2017 Jason Wallace
Diepenbrock, CH, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.17.00475
   Novel loci underlie natural variation in vitamin E levels in maize grain

The authors investigated tocochromanol synthesis in all 5000 members of the maize Nested Association Mapping population. Tocochromanols are important antioxidants in seeds that contribute to seed viability, and in the diet they constitute a source of Vitamin E. The authors identified 52 QTLs for one or more tocochromanol traits, including 14 that resolve to individual genes. Six of these genes have activities not before associated with tocochromanols, including chlorophyll biosynthesis genes. Many of the QTL have a significant impact on the levels of one or more tocochromanol compounds, including showing epistatic interactions. Understanding how these genes interact in grain tocochromanol synthesis should enable them to be used in biofortification breeding schemes. Jason Wallace, 2017




11/2017 Lin Li
Li, X, et al. 2017. Nature communications. 8:991
   Single nucleus sequencing reveals spermatid chromosome fragmentation as a possible cause of maize haploid induction

The doubled haploid (DH) technology enables generating completely homozygous lines in just two generations and, thus, has been widely used in modern genetics and breeding. However, the molecular mechanisms of the core technique ��� haploid induction is largely unclear. Li and colleagues employed an very sophisticated technique combining single nucleus isolation and high-throughput sequencing, and traced the genomic structure variation during double fertilization after the pollination of inducer pollen. This study provides a detailed molecular view of spermatid chromosome fragmentation during haploid induction, which supports the hypothesis of fertilization first followed by chromosome elimination since paternal DNA fragments. This study largely furthered our understanding of molecular mechanism of haploid induction in plants. Lin Li, 2017




11/2017 Fang Bai
Dong, Z, et al. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1714960114
   Ideal crop plant architecture is mediated by tassels replace upper ears1, a BTB/POZ ankyrin repeat gene directly targeted by TEOSINTE BRANCHED1

The teosinte branched1 (tb1) encodes a class II TCP transcription factor which is known to repress the tillers and aerial axillary branches development. Teosinte is the wild ancestor of maize which has highly branched tillers and aerial parts. Domesticated maize contains a natural gain of function allele of tb1 which reduced the branch and increased the yield. In this paper, authors screened the mutants with the similar phenotype of tb1. Dong et al. cloned the gene tassels replace upper ears1 (tru1) by chromosome walking and found that TRU1 encodes an ankyrin repeat domain gene containing a BTB/POZ motif. Using genetic cross of tb1 and tru1 mutants combined with the immunolocalization experiments, they found that TRU1 and TB1 function in the same pathway. Further chromatin immunoprecipitation (ChIP) and qPCR confirmed the direct interaction of the BTB/POZ domain ankyrin repeat protein and TB1. The significant of this paper is that the authors found a genetic mechanism of the domesticating of teosinte to modern crop. Fang Bai, 2017




10/2017 Ruben Rellan-Alvarez
Kusmec, A et al. 2017. Nature Plants 3:715-723
   Distinct genetic architectures for phenotype means and plasticities in Zea mays

Plasticity, the ability to express different phenotypic responses to varying environmental conditions and robustness, and the ability to maintain a developmental program in a diverse set of environments are conflicting choices that plants need to address. Plasticity as a trait is under genetic control and variation QTLs have been studied in a number of species and is of great interest for plant breeders that want to understand what are the genetic components explaining trait plasticity over different environments. In this paper, Kusmec and collaborators used the 5000 RILS of the NAM mapping population and measured 23 agronomic traits in multiple environments. Using a Finlay-Wilkinson regression that calculates a regression line for a trait in a given line and environment and compares it with the average value of all the lines for that trait in that given environment. Using this approach the authors were able to dissect the genetic components explaining plasticity and mean values of all the traits they evaluated and show that different genes control plasticity and mean values and open the opportunity to be able to breed for both plasticity and robustness. Ruben Rellan, 2017




10/2017 Lin Li
Li, Q, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.17.00576
   The maize imprinted gene Floury3 encodes a PLATZ protein required for tRNA and 5S rRNA transcription through interaction with RNA polymerase III

The authors cloned the classical mutant floury3 and validated that an Asn to His replacement in PLATZ (plant AT-rich sequence- and zinc-binding) protein is the causal mutation. Genetic experiments indicated that Floury3 is a specially expressed in maize starchy endosperm cells and regulated by genomic imprinting. Floury3 interacts with PRC53 and TFC1, which are the key components of the RNA polymerase III (RNAPIII) transcription complex. The causal mutation in Floury3 could impair the function of RNAPIII, which reduces the levels of many tRNAs and 5S rRNAs, and further lead to defects in endosperm development and storage reserve filling in maize floury3 seeds. It is the first report on the genetic and functional role of PLATZ transcriptional factors in plants. Lin Li, 2017




10/2017 Jason Wallace
Bedoya, CA, et al. 2017. PLoS One. 12:e0173488
   Genetic diversity and population structure of native maize populations in Latin America and the Caribbean

The authors profiled 194 maize populations from across Latin America and the Caribbean to characterize the relationships among these accessions. The landraces fell into three main groups: one that includes Mexico and the southern Andes (due to both pre- and post-Columbian movment of germplasm between the two), a lowland Mesoamerican and Caribbean group, and an Andean group that has remained relatively isolated from the other two. Each group was further divided into subclusters based on within-group genetic diversity, with 3-9 subclusters per group. The authors also relate the patterns of variation to proposed routes of human migration through Latin America. Jason Wallace, 2017




10/2017 Fang Bai
Chen, JY, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.17.00099
   Zygotic genome activation occurs shortly after fertilization in maize

With the rapid development of the global transcription study, thousands of genes were reported to involve in the embryogenesis in flowering plants. However, the study of the onset of zygote genome activation (ZGA) in crops is limit. In this paper, Chen et al. generated transcripts from the male and female gametes, and the zygotes at the different hours after pollination in maize. They compared the maize transcriptomes to those published RNA-Seq data from rice sperm and egg cells, and found the conserved genes involved in the gametogenesis and embryogenesis. To characterize the onset of ZGA, they analyzed the transcription profiles of the sperms, eggs and the zygotes at early stages, and found that ZAG happened shortly after the fertilization. They further studied the transcription factors in gametes and zygotes, and examined some homeodomain genes that activated in embryo patterning. Since the cell cycle regulation during zygote development, the authors investigated the expression patterns of 443 important cell cycle regulator genes in games and zygotes and determine the timing of zygote development in maize. In addition, they analyzed the auxin regulated genes and some cell signaling genes in early embryo patterning in maize. The significance of this paper is that they detailed analyzed the timing of zygote development and generated RNA-Seq transcriptome profiles of gametes and zygote cells which will provide the comprehensive dataset for the research community and future crops study. Fang Bai, 2017




9/2017 Fang Bai
Yang, Q, et al. 2017. Nature Genetics. 0:doi: 10.1038/ng.3919
   A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens

Maize is one of the most important economic plants in the world and the major crop in U.S. However, fungal disease severely damaged the plants during the plant development and largely reduced the crop yields. Recently, several disease-resistance quantitative trait loci (QTL) in maize have been studied and seven maize disease-resistance genes were identified and published. One of the disease-resistance QTL named qMdr9.02 is on the chromosome 9 in maize. qMdr9.02 has been shown to be associated with resistance to three foliar fungal diseases in maize: southern leaf blight, gray leaf spot and northern leaf blight. In this paper, Yang et al. mapped the B73qMdr9.02 to a small window around 100-kb interval on chromosome 9 by repeated backcrossing of NC292 to B73 with marker-assisted selection. The authors did specific association analysis and expression experiment for the candidate genes in qMdr9.02 region. With the help of transgenic lines and the disease resistant experiments, they identified a caffeoyl-CoA O-methyltransferase (CCoAOMT) gene,ZmCCoAOMT2, is the gene that give the resistance effect at qMdr9.02. By using liquid chromatography-mass spectrometry (LC-MS), the authors found that ZmCCoAOMT2 controls metabolite levels in the phenylpropanoid and lipoxygenase pathways. In addition, ZmCCoAOMT2 may function in disease resistance by suppressing the program cell death. This significant discovery indicates a way in the future to improve the crop disease-resistance and increase the crop yield. Fang Bai, 2017.




9/2017 Jason Wallace
Swarts, KL, et al. 2017. Science. 357:512-515
   Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

Maize arrived in the lowlands of what is now the Southwestern United States ~4000 years ago but did not achieve widespread cultivation in the highlands until ~2000 years later. This delay is hypothesized to be due to poor adaptation of tropical maize to the short growing season of upland areas. Swarts et al. tested this hypothesis by sequencing ancient DNA from right after upland maize cultivation became widespread and using modern maize landraces and inbred lines to predict the phenotypes of these ancient varieties. They found that the ancient maize was partly adapted to earlier flowering (faster than tropical varieties but not as fast as modern fast-flowering varieties). The ancient varieties were also predicted to be shorter and bushier (with more extensive tillering) than modern varieties. The segregation patterns of regions that appear to be selected for flowering indicate that shorter flowering was selected by combining standing variation rather than from novel mutations. Jason Wallace, 2017




9/2017 Lin Li
Leng, PF, et al. 2017. Molecular Plant. 0:doi: 10.1016/j.molp.2017.07.013
   Auxin binding protein 1 reinforces resistance to sugarcane mosaic virus in maize

After cloning the resistant gene ZmTrxh (Scmv1) to Sugarcane mosaic virus in maize, the collaboration by Mingliang Xu Lab from China Agricultural University and Thomas Lübberstedt Lab from Iowa State University published the work on cloning ZmABP1, which is the other resistant gene to Sugarcane mosaic virus. There are two major QTLs conferring the resistance to Sugarcane mosaic virus in maize. ZmABP1 is the functional gene of Scmv2. Moreover, ZmABP1 could enhance the resistant effect of ZmTrxh. ZmABP1 encodes a Auxin Binding Protein. The causal SNP mutation in ZmABP1 could result in the differentially expression of ZmABP1, which leads to the resistance to Sugarcane mosaic virus in maize. The discovery of ZmABP1 and ZmTrxh furthers the understanding of resistance mechanism to virus in plants and will benefit maize breeding on the resistance selection. Lin Li, 2017

This paper shows that the gene scmv2 is the same as the gene abp1. That is, abp1 is the gene responsible for scmv resistance contributed by scmv2. This was confirmed by the authors to MGDB curator staff. The gene model is GRMZM2G116204




9/2017 Ruben Rellan-Alvarez
Studer, AJ et al. 2017. Genetics 207:755-765
   Selection during maize domestication targeted a gene network controlling plant and inflorescence architecture

There are currently no comments for this article.


8/2017 Ruben Rellan-Alvarez
Zhang, Y et al. 2017. Plant Cell pp.doi: 10.1105/tpc.17.00354
   Differentially regulated orthologs in Sorghum and the subgenomes of maize

There are currently no comments for this article.


8/2017 Jason Wallace
Tan, BC, et al. 2017. Genetics. 206:135-150
   Structure and origin of the White Cap locus and its role in evolution of grain color in maize

White Cap is a dominant genetic locus that turns yellow maize endosperm white. The authors localized the Wc locus to a tandem duplication of up to 23 copies of a Carotenoid clevage dioxygenase 1 gene (Ccd1). The authors propose a model where a duplication first created a second copy of Ccd1 and surrounding genes, followed by tandem expansion due to unequal crossing-over between Tam3L transposons in the new cluster. Although Wc is most visible in yellow-endosperm maize the alleles are most common in white varieties (and absent in teosinte). The authors propose that Wc intensifies the whiteness of already white kernels, which could have been the basis for human selection. Jason Wallace, 2017




8/2017 Lin Li
Strable, J, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.16.00477
   Maize YABBY genes drooping leaf1 and drooping leaf2 regulate plant architecture

Ideal plant architecture is a key contributor to high yield of modern maize production. Accompanied with the increase of maize yield, maize leaf angle showed a vital change, which made an ideal canopy structure for high density of maize planting. However, the genetic architecture has not been fully addressed. In this study, Strable and colleagues uncovered two drooping leaf mutants, which showed pleiotropic mutations affecting leaf length and width, leaf angle, and internode length and diameter. A series of genetic experiment, including bulked analysis, fine-mapping, and allelism test etc, identified the causal genes, which are paralogous YABBY genes. Following functional analyses such as histological, scanning electron microscope analyses, RNA hybridization etc, demonstrated that drl genes control elaboration of leaf patterning and further shape leaf architecture in maize. Quantitative analysis in NAM-RIL population also validated that drl loci had the quantitative variation for leaf and stem traits, indicating that these drl loci have not been fixed during the modern breeding and will be good targets for the future selection in maize breeding. Overall, this study provides us a solid link for the function of YABBY genes in the shaping of maize architecture, and furthers our understanding of the genetic architecture of maize plant architecture. Lin Li, 2017




8/2017 Fang Bai
Kim, Eun-Deok, et al. 2017. Sci. Rep.. 7:3838
   Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development

Endosperm is a persistent structure and the main food resource for the embryo during the maize seed development. Endosperm has four cell types: aleurone (AL), starch endosperm (SE), embryo surrounding region (ESR), and basal endosperm transfer layer (BETL). In this paper, Kim et al. studied the coding and long noncoding transcripts from AL, SE and BETL at three different developmental stages. Based on the RNA-seq analysis, they found that both coding and non-coding transcripts were more abundant in BETL than other two cell types, and they played regulatory roles in the endosperm cell differentiation. The authors further classified spatio-temporal transcripton clusters and analyzed their functions using GO term analysis. They studied the spatio-temporal epigenetically regulation of imprinting and found that maternally expressed genes (MEGs) enriched in AL and BETL, and paternally expressed genes (PEGs) enriched in BETL. Kim et al. also examined the enrich region of H3K27me3, an epigenetic marker, by chromatin immune-precipitation (ChIP) followed by sequencing. They showed that the transcripts from H3K27me3-enriched loci were over-represented in BETL transcriptom. Fang Bai 2017




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. PLoS One 12:e0184202
   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 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




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.




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 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 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 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 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 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




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 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




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: https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA244661




3/2017 Jason Wallace
Hirsch, CN et al. 2016. Plant Cell 28:2700-2714
   Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Download the assembly here: http://datadryad.org/resource/doi:10.5061/dryad.8vj84

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 http://nrgene.com.

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 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: https://www.ncbi.nlm.nih.gov/sra/?term=SRP077851 Philipp R Weckwerth, 2017




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 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): https://www.ncbi.nlm.nih.gov/sra/?term=SRA504653




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 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




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 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 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