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

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

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

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 ug/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.

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

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

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

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.

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

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, maizesequence.org) 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

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

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

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.

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

Establishing cell polarity is critical in many aspects of plant development, including asymmetric cell division and polar tip growth in root hairs or pollen tubes. In maize and other grasses, the stomatal complex is formed by a series of asymmetric divisions that produce the guard cells and subsidiary cells that surround them. Previously, the maize leucine-rich repeat receptor-like kinase PANGLOSS1 (PAN1), was shown to play a key role in this process. This paper significantly adds to our understanding of the mechanism of PAN1-dependant polarization of maize subsidiary cells. The authors show that plant Rho GTPases (ROPs), which are known to mediate polarity in other developmental contexts, also regulate polarity of subsidiary cells downstream of PAN1. Interestingly, ROPs were shown to localize to the same domain as PAN1, and this localization was PAN1 dependent, suggesting that these ROPs polarize downstream of PAN1. In spite of this, rop mutants enhance the pan1 phenotype indicating that ROPs can still polarize subsidiary cells independently of PAN1. These findings raise interesting questions regarding the evolution of novel polarity establishing pathways. The assymetric division of subsidiary cells is a relatively recent innovation in the Poaceae. Was PAN1 involved in other polarity processes before subsidiary cells arose? If not, how did PAN1 integrate with ROPs to gain a novel polarity role? As more pieces of the subsidiary cell polarity pathway emerge, such questions can begin to be addressed. Clinton Whipple, 2011

Reduced leaf expansion in response to water deficit has two components: response to evaporative demand, or relative humidity, and response to soil water deficit. Leaf expansion slows or ceases in response to either condition. The authors set out to build evidence to answer an important question: Are the mechanisms controlling response to soil water deficit and response to evaporative demand common, or do completely separate mechanisms exist? The authors used a QTL mapping approach and looked for overlapping QTLs detected under each condition. To achieve separation of conditions, highly controlled greenhouse experiments were conducted and leaf growth was monitored every 15 minutes with a specialized greenhouse phenotyping platform. Three mapping populations were used along with several sets of introgression lines. First of all, the authors found an abundance of variation in response to these conditions. For some RILs, growth ceased under water deficit values three-fold greater than for other RILs. Many QTL (50% of QTLs) were common to both types of sensitivities, suggestion overlap in mechanisms controlling leaf growth in response to both types of water deficit. Aaron J. Lorenz, 2011

Decades ago a dicentric chromosome was formed due to a translocation between chromosomes 1 and 5. Subsequently, this translocation was stabilized by the spontaneous inactivation of one of the two centromeres. Gao et al. have demonstrated that the inactive centromere still retains the CentC satellite repeats and CRM centromere-specific retrotransposon sequences, but does not condition a functional centromere. The authors found that this inactivated centromere does not form a constriction on the chromosome, is not bound by CENP-C, and does not contain the histone H3 modification of phosphorylation on serine 10. This finding reiterates the point that the presence of CentC and CRM sequences are not sufficient to condition the formation of a functional centromere, even in the same nucleus where other centromeres with the same sequences are functional. Therefore, the specification of the kinetochore and incorporation of CENP-C to regions of chromosomes that contain CentC and CRM sequences involves a sequence-independent epigenetic mechanism that cannot be specified in trans by another centromere. Keith Slotkin, 2011

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

Few topics are hotter than the search for alternative energy sources that are renewable, efficient and cost-effective. The myriad ways plant material could be used as a source of biofuel to replace or supplement petroleum-based fuels are the focus of several national research initiatives. Many sound ideas are being tested but, to-date, commercial success appears a distant promise. Chuck and co-authors report a significant advance in overcoming a barrier for one biofuel strategy - the production of ethanol from the biomass of perennial grasses. They used the maize Corngrass1 (Cg1) tandem microRNA gene to extend the juvenile phase of development in several plant species, including switchgrass (Panicum virgatum), favored as a potential bioenergy crop. Overexpression of Cg1 affected several plant characteristics, including increased branching, prolonged juvenile growth and delayed flowering. Although driven by the maize ubiquitin promoter, Cg1 overexpression in switchgrass produced three phenotypic classes: severe, moderate and weak. The weak class had increased biomass, up to 250% increased starch content in stems and never flowered. Modification of all these traits allowed for an increased and more efficient production of glucose that would be used for fermentation. This paper illustrates the power of maize as a model system to test the hypothesis that modulating juvenile development could improve the biofuels properties of a feedstock species moving it a step closer to commercial viability. Mike Muszynski, 2011

The KNOTTED1 protein of maize is an important transcription factor for shoot apical meristem maintenance and acts non-cell autonomously, trafficking to neighboring cells. However, the KNOTTED1 protein is too large to diffuse through the plasmodesmata size exclusion limit, and therefore it was previously demonstrated that selective trafficking occurs to move particular proteins or other substrates of large size through plasmodesmata to neighboring cells. Xu et al have made important progress in understanding selective trafficking of KNOTTED1 and other transcription factors through plasmodesmata. They engineered an Arabidopsis reporter system of plasmodesmata trafficking based on the non-cell autonomous rescue of a trichome mutant phenotype using fragments of the maize KNOTTED1 protein. Once established, they mutagenized this system and found that a chaperonin subunit, CCT8, is necessary for selective trafficking of KNOTTED1 and other transcription factors. Their data suggests that this protein is required to unfold the selectively trafficked protein upon arrival through the plasmodesmata in the recipient cell. This data provides an important step into understanding how selective trafficking occurs, and why some proteins are selectively trafficked while others are not. R. Keith Slotkin, 2011

Maize was domesticated from the wild grass teosinte, which grows natively in Mexico. There is, however, significant diversity among the Mexican teosintes including annual, perennial, diploid and tetraploid taxa. Current taxanomy includes five teosinte species: Zea perennis (tetrapoloid perennial), Z. diploperennis (diploid perennial), Z. luxurians (diploid annual), Z. nicaruagensis (diploid annual), and Z. mays (diploid annual). Maize (Z. mays ssp. mays) was domesticated from the annual diploid teosinte species Z. mays. This paper adds to this diversity by describing three new populations of teosinte that are different enough from currently described species to be considered new species. The potentially novel species include a diploid annual from Oaxaca, a diploid perennial from Nayarit, and a tetraploid perennial from Michoacan. While the phylogenetic analyses were not quite large enough to fully resolve all the relationships among Zea species, this study further underscores the diversity that exists among teosintes and the need for more extensive analyses. As the authors point out, maize experienced a genetic bottleneck during domestication and many potentially useful alleles are likely harbored among the teosintes. Resolving the relationships among the teosintes will be key to preserving this important germplasm. Clinton Whipple, 2011

As maize yields are pushed to the limit, resource utilization efficiency traits increase in importance because yield is increasingly likely to be limited by a specific resource. Water use efficiency and nitrogen use efficiency are hot topics these days. The manuscript I selected this month seeks to develop an understanding of the genetics controlling phosphorous use efficiency, a resource use efficiency trait that receives relatively little attention. One of the biggest challenges researchers face when studying a resource use efficiency trait is developing growing conditions in which the trait can be observed. In this study, low and high phosphorous sites were identified for the experiment and the high phosphate sites were fertilized with additional phosphate to obtain contrasting growing conditions. It appears that these conditions were adequate because significant differences in grain yield and other agronomic traits were observed. The six inbred lines used were well suited to this study because they were selected from a phosphorus use efficiency breeding program to create set of inbreds with a range phosphorus use efficiencies. The authors carried out a generation means analysis a powerful design in which the inbreds, their F1s, F2s and Backcrosses are all compared. In addition to grain yield, grain phosphorous content, stover phosphorous content and anthesis silking interval were measured. Using these traits together with information about the soil phosphorous content, the authors derived additional traits related to phosphorous use efficiency. The resulting data are analyzed using standard quantitative genetics methods and the authors interpret their results in terms of specific recommendations for breeders interested in improving phosphorous efficiency utilization. On the whole, I found this paper to be a thorough treatment of difficult subject matter and an excellent example of how a well-designed experiment can lead to specific recommendations with real-world value. Paul Scott, 2011

For those that experienced both record heat and drought during this summer pollinating season, you have first-hand knowledge of how critical heat and water stress can be on having a successful crop. Virlouvet and co-authors take a full bore approach to dissect a portion of the molecular mechanisms underlying how the maize plant responds to water deficits by characterizing both the Zea mays abscisic acid- (ABA), stress- and ripening-induced (ZmASR) gene family and how over expression of a key family member, ZmASR1 leads to increased biomass accumulation and grain yield under normal and water limited conditions. ZmASR1 was initially indentified as a candidate protein underlying a QTL controlling leaf senescence and anthesis-silking interval in a RIL population grown under a water deficit. Using the complete B73 reference genome, a total of 9 ZmASR genes were identified with several members responding to both water deficit and other stress treatments as measured by transcript and protein accumulation. Constitutive expression of ZmASR1 in transgenic maize affected several traits leading to drought tolerant yield gains. Comparative analysis of transcriptomic, proteomic and metabolomic profiling results from transgene plus and minus sib plants under normal and water-limiting conditions indicated a link between the biosynthesis of specific amino acids and other metabolites with growth rate. Such results are encouraging but merit further analysis of this transgene in commercially elite germplasm. Overall, this paper exemplifies a well balanced approach that leads to increased understanding of the basic biology of stress responses in maize and also an application of this new knowledge that may protect yield in a crop under water-stress. Mike Muszynski, 2011

QTL effect-by-genetic background interaction can hinder marker-assisted breeding because marker effects are not consistent across breeding populations and therefore need to be estimated for each breeding population separately. The authors find QTL-by-genetic background interactions for grain yield and grain moisture within a series of connected European bi-parental breeding populations. They found that the most powerful way to detect QTL was to model the marker effect as a nested effect within breeding population, effectively allowing each allele to have a different effect in each population. A model simply ignoring breeding population was inferior for detecting QTL. Both models were better than performing a simple QTL analysis within each bi-parental population separately. Combining data across populations improved power as well as resolution. This study displays the benefits of multiple-population (or "multiple-line cross" as in the title) QTL analysis relative to simple bi-parental QTL analysis. Also, this paper highlights the fact that advanced marker-based selection methods such as genomic selection may benefit from capturing allele-by-genetic background information. Aaron Lorenz, 2011

You have cloned your favorite mutant and find the gene is a member of a larger gene family. What's your next step? One option is to characterize the entire family. This paper describes the comprehensive characterization of a particular sub-family of transcription factor that contains a homeodomain and leucine zipper, the HD-ZIP IV family. This gene family has been found in all land plants and several members have epidermal-related function and/or expression. Javelle and co-authors characterized the phylogeny, synteny, gene structure, expression and regulation of the 17 HD-ZIP IV genes from maize. As with most maize genes, about half of the HD-ZIP IV's are paralogs, duplicated after maize and sorghum last shared a common ancestor. Of the members where expression was detected, most are expressed in immature reproductive organs and many show a preference for expression in the epidermis. Interestingly, 13 of the 17 genes have two short conserved motifs in their 3' UTRs, indicating they may be regulated by small RNAs or secondary structure formed by these motifs. This paper exemplifies how to characterize a gene family in maize and lays the foundation for analysis of individual member function. Mike Muszynski, 2011

Working in our summer nursery a couple of weeks ago, I noticed that the plants were a little dry, so I turned on the drip irrigation for the night and went home. I woke up in the early hours of the morning to a loud thunderstorm with a lot of wind. When I arrived at my field the next day, my worries were confirmed as most of the corn had been knocked flat during the night. I knew that the stalks will eventually recover, and I have watched them gradually return to an upright position. I had not given much thought to how maize plants manage this fortunate recovery until reading this paper. Lodging is a source of significant yield losses, not just for maize but also other cereals. Zhang et al. investigate how differential growth of pulvini, the bulbous region at the nodes of the stalk, respond to gravity and return the plant to an upright posture. The pulvini of nodes 9-12 respond to gravity by differentially elongating their cells, with more elongation in the lower region of the pulvinis, which then pushes the stem back towards the sky. This paper takes a detailed look at changes in upper and lower pulvini regions in response to gravistimulation. This includes an analysis of cell wall composition, hormone content, as well as transcript and metabolite profiles. The authors found siginificant changes in cell wall components, particularly lignin, heteroxylan, xyloglucan and heteromannan. They also found significant changes in the levels of the hormones auxin, GA and ABA. These changes were corroborated by the transcriptome and metabolome profiles. The implication of auxin is perhaps not surprising since it is classically known to regulate differential growth in response to environmental stimulation. Interestingly maize mutants like baf1, fail to make analogous pulvini in the tassel, where they function to increase the angle of tassel branches. It would be interesting to investigate pulvinus response to gravistimulation in baf1 and other known maize auxin mutants. Clint Whipple, 2011

Maize kernels are normally translucent, so if you put them on a light box, light comes through them. In opaque mutants, light is not transmitted through the kernels. Many mutants have an opaque phenotype, suggesting that there are a lot of ways to make opaque kernels. Several mutations with opaque phenotypes have been characterized molecularly and the majority of them are involved in some aspect of seed storage protein deposition. This paper caught my eye because it describes molecular characterization of an opaque mutant (o5) that encodes a monogalacotsyldacylglycerol (MGDG) synthase, an enzyme involved in lipid biosynthesis. The authors present a body of evidence supporting the hypothesis that plastid membrane lipid composition is perturbed in this mutant and these perturbations result in altered starch granules that may explain the opaque phenotype of the kernels. The story is complicated by developmental aberrations in several tissues, emphasizing the importance of membrane structure in development. An explanation of the results was not immediately apparent to me, however the discussion section was particularly satisfying because it draws the results together with previous results into a detailed and reasonable hypothesis that will undoubtedly be a valuable in future studies. Thus, another mechanism for generation of opaque kernels has been characterized, illustrating the molecular complexity of this visually simple trait. Paul Scott 2011

In this manuscript PCR products were amplified while linked to inherently fluorescent quantum dots (QDs) in a one-to-one ratio. PCR with QDs was a technical challenge, which was overcome by attaching one PCR primer to the QD prior to amplification of a long (400-500bp) DNA strand. The QDs have brighter and more stable fluorescence compared to organic fluorophores, and these probes have great potential for quantitative measurement of nucleic acid in FISH, Southerns, Northerns, etc.. The authors demonstrated this utility by attaching a 480bp fragment of the maize fatty aldehyde dehydrogenase 1 (rf2eI) gene to the QDs and performing FISH on maize prometaphase, metaphase and interphase chromosomes. The QD probe detected two brightly fluorescing loci at the known location of rf2eI at each of these stages. R. Keith Slotkin, 2011

doi: 10.1104/pp.111.174748

The Intermated B73-Mo17 (IBM) population is widely used population for QTL mapping and studies on the genomic architecture of maize. These authors developed a population of near-isogenic lines from the inbreds B73 and Mo17 to compliment the IBM population. One hundred lines were derived from using B73 as the recurrent parent, and 50 lines were derived from using Mo17 as the recurrent parent. Careful analysis of array-based genotype data revealed some interesting findings with respect to the genomic architecture of maize. First, many genomic regions that showed an elevated number of B73 introgressions also showed fewer Mo17 introgressions. Likewise, genomic regions that showed an elevated number of Mo17 introgressions also showed fewer B73 introgressions. This result, combined with segregation distortation data in the IBM population, indicates loci with bias towards either the Mo17 or B73 allele. Secondly, the amount of residual heterozygosity was greater than expected, particularly in the centromeric regions of low recombination. This finding agrees with the observation in the NAM population of McMullen et al. (2009) and provides further evidence for the Hill-Robertson effect on heterosis. Finally, the authors determined if Mo17-specific amplifications mapped to the same location as the original B73 sequence, or if they mapped to unlinked regions. They discovered a preponderance of unlinked copy number variants. This characteristic of maize genomic variation likely stems from the ancient genome duplication event and subsequent fractionation of gene pairs, or transposon-mediated duplication. This study further characterizes the vast genomic variability of maize, which gives rise to our ability to improve maize through breeding and selection. Aaron Lorenz, 2011

Roughly 10,000 years ago the plant that we know today as maize was being domesticated from wild teosinte (Zea mays ssp. Parviglumis). Previously, the work of John Doebley and others have identified just a few major QTLs responsible for the seemingly large morphological differences between maize and teosinte. One of the morphological differences is in the number of axillary branches that grow out, with maize having increased apical dominance compared to teosinte. The gene that controls this phenotype is teosinte branched 1 (tb1), a TCP family transcription factor that is not mutated in maize, but rather expressed at twice the rate compared to teosinte. The regulatory region responsible for the transcriptional differences in tb1 were previously mapped ~60-70kb upstream of the coding region. Zhou et al have investigated this region from hundreds of maize, teosinte, and association panel diversity lines and found a striking connection between apical dominance and DNA sequence. These authors identified two transposable element insertions that correlate with the transcriptional differences of the tb1 gene between maize and teosinte. These insertions are present in some teosinte lines, and were selected for due to their promotion of apical dominance in maize. This manuscript provides and powerful example of how genetic diversity produced by a transposable element-generated gain-of-function allele was utilized and selected for by the domesticators of modern maize. R.Keith Slotkin, 2011

Expediting the development of crops with increased tolerance to limited water conditions is critical in the face of increased competition for water and climatic variability. Setter et al. (2011) took a candidate gene association mapping approach to identifying SNPs correlated with favorable response to drought. The association mapping panel used was diverse enough to allow resolution at the gene level. The authors evaluated 350 tropical and subtropical inbred lines for metabolite traits under well-watered (WW) and water-stressed (WS) conditions. Candidate genes were chosen based on their putative involvement in metabolic pathways and regulatory systems controlling reproductive development during drought. A negative correlation between abscisic acid (ABA) and ear and silk dry weight was found, in agreement with ABA's role in energy conservation in response to plant stress. One of the strongest SNP-trait associations was between a SNP within an aldehyde oxidase gene and ABA concentration in the silk under WS conditions. Other associations between SNPs within candidate genes and metabolite traits were identified. This study shows how dissecting response to drought, a highly complex trait, into component metabolite traits and associating those traits with marker variants can help identify genes with potential for improving drought tolerance. More studies such as this are needed to provide the knowledge needed to most effectively mine maize germplasm collections for rare alleles conferring enhanced drought response. Aaron Lorenz, 2011

Development of the maize endosperm and single-cell layer aleurone offers a model system in which to study the network of cell specification signals controlling differentiation of these two tissues. Yi et al. add to this network by identifying the thick aleurone1 (thk1) mutation and characterizing its function in aleurone cell specification. Kernels mutant for thk1 produce additional layers of aleurone cells and are embryo lethal. This is in contrast to dek1 mutant kernels that lack any aleurone cells but also have aborted embryos. How does one study two mutations with contrasting phenotypes that cannot produce viable mutant plants? This manuscript showcases the richness of genetic tools available in maize that were used to study thk1 function and its interaction with dek1. Using B-A translocations for mapping, chromosome breaking Ds and Ac lines for sector analysis, epistatic interactions and double-mutant sector analysis, the authors were able to show thk1 defines a negative regulator that functions downstream of dek1 in aleurone specification. The thk1 mutation was caused by a deletion encompassing about 2 megabases and so its molecular nature has yet to be identified. Michael G. Muszynski, 2011

A clear consensus has emerged that maize (Zea mays ssp. mays) was domesticated a single time in Mexico from annual teosinte (Zea mays ssp. parviglumis). However, genetic and archeological evidence have been inconclusive about the region of domestication within Mexico. The most ancient remains of domesticated maize have been found in lowland Mexico, and this is also where current parviglumis populations are found. However, previous genetic analyses suggested that domesticated maize from the highlands is more closely related to parviglumis than is maize from the lowland varieties, pointing toward a highland origin for maize. This paper reexamines the genetic evidence for the region of maize domestication by analyzing a large SNP (single nucleotide polymorphism) dataset obtained from maize (Z. mays ssp. mays), and two teosinte subspecies, Z. mays ssp. parviglumis and Z. mays ssp. mexicana. Their analysis indicated a large amount of introgression between highland maize and ssp. mexicana, which also occurs in the highlands. Thus it is possible that the apparent close relationship of highland maize to ssp. parviglumis may be an artifact of later introgression of teosinte alleles from ssp. mexicana. Indeed, when this introgression is controlled for, maize from the lowlands is the closest to ssp. parviglumis. Thus it appears that when introgression of ssp. mexicana is taken into account, the genetic evidence confirms archeological and biogeographical evidence that maize was domesticated in the lowlands. Clinton Whipple, 2011

The start of another pollinating season is upon us in the Midwestern USA and in honor of this occasion I selected a paper relevant to pollination. Maize cells are surrounded by a rigid cell wall, yet when a pollen grain lands on a silk a pollen tube grows between the cells of the silk to deliver the pollen nuclei to the egg. How does the pollen tube work its way between the rigid cell walls of the silk? The hypothesis tested in this paper is that a family of proteins in pollen called beta-expansins modifies the cell walls of the silk so they can be deformed by the pollen tube as it travels down the silk. Expansins are known to function in cell growth by altering the cell wall to allow cells to expand. Beta-expansins are expressed at high levels in pollen, making this hypothesis a reasonable one. The authors carried out an extensive set of biochemical experiments in which they treated silk cell wall preparations with beta expansin purified from maize pollen. Characterization of the resulting products allows the authors to conclude beta expansins alter cell wall structure. Moreover, grass cell walls seem to be altered in a specific way. Several physical properties of cell walls treated with beta expansins were examined as well with results consistent with a role for beta expansins in creating flexibility in the cell wall. Intriguingly, the mechanism of beta-expansin- induced modification does not appear to be enzymatic. This seems reasonable, since some aspects of cell wall formation (polymerization of lignin for example) proceed by non-enzymatic mechanisms. The biochemical details of the effect of beta-expansin treatment of cell walls provide important insights into the mechanism of pollen tube growth in maize silks. Paul Scott, 2011

Researchers often use model species to answer biological questions. One question that arises from this practice is: How relevant is information from a model species to other species? For example, the model species Arabidopsis thaliana is a dicotyledonous species of no agricultural importance, while maize is a monocotyledonous species that produces more than $20 billion worth of grain each year in the US. In this paper, information from Arabidopsis was used to design transgenic plants with increased oil content, a modification of potentially great commercial value. The Wrinkled1 transcription factor was initially characterized in Arabidopsis and shown to be involved in controlling oil deposition in seeds. This manuscript reveals an interesting comparison and contrast between oil biosynthesis in Arabidopsis and maize. In Maize, two wrinkled1 homologs exist and both of these genes functionally complement the Arabidopsis gene. Overexpression of one of these genes in maize has been shown to increase oil content of the seed (Shen et al., 2010 Plant Physiol 153:980-987). In this new work, transgenic maize plants overexpressing one of the wrinkled1 homologs from maize (ZmWri1a) transgenic plants are analyzed in more detail, revealing effects on metabolites and genes involved in oil biosynthesis. Intriguingly, many of the genes identified as having altered expression in the transgenic plants carry a DNA motif called the AW box in their promoter. This sequence has been shown to be the Wrinkled1 binding site in Arabidopsis. Thus it seems that Arabidopsis is an excellent model for oil biosynthesis in maize and insights can be readily transferred to achieve beneficial results. Paul Scott, 2011

There is very good evidence that alleles conditioning resistance to multiple plant pathogens exist and can be an important, stable source of disease resistance. Wisser et al. (2011) used a maize diversity panel and mixed models approach to show that a substantial proportion of the genetic variation for resistance to three maize fungal diseases is generated by multiple disease resistance alleles. After correcting for days to anthesis and populations structure, the genetic correlation between these three diseases was still greater than 0.50 for all three disease pairs. Linkage disequilibrium decays within 1500 bp for most genic regions in this diversity panel, which is shorter than the average length of a maize gene. For this reason, the authors inferred that the relationship between these different disease resistances is caused by pleiotropy rather than linkage. An association analysis was performed using only 858 SNPs along with a multi-variate model in order to detect SNPs associated with multiple disease resistance. Surprisingly, three associations were made that exceeded the significance threshold adjusted for multiple testing. The strongest of these associations occurred with a SNP located within a glutathione S-transferase gene family member. These genes have been previously implicated in general disease and stress resistance. Re-sequencing of this gene for 139 to 185 panel members confirmed this association. The allele substitution effect of the mostly strongly associated SNP was quite small, only being ~6% of the range of the disease rating scale used. This paper provides more valuable knowledge in the area of stable disease resistance, which is desperately needed to maximize crop yields and stave off losses from increasing pathogen pressures.

Biotrophic fungal pathogens often alter developmental fate of their host plants in order to survive and reproduce. This is the case with Sporisorium reilianum which causes head smut in corn and may be familiar to maize researchers who have seen the stunningly deformed tassels and ears on infected plants. To better understand the mechanisms by which this fungus alters development, the authors performed detailed morphological and transcriptional analyses on infected plants. They found fungal infection altered inflorescence development in specific ways leading to (1) a loss of apical dominance in axillary branches, (2) conversion of floral organs into leaf-like organs (phyllody) leading to complete reversion of the inflorescence to a vegetative state and (3) loss of meristem identity and determinacy, resulting in spikelets initiating inflorescence meristems. Transcript profiling of inflorescences early in the infection process, prior to obvious developmental alterations, identified expression changes in developmentally important transcription factors, hormone biosynthetic genes and genes responsive to increases in reactive oxygen species. Although this work is a first step to dissect the mechanisms that alter developmental fate of the host by this pathogen, since both the maize and S. reilianum genomes have been sequenced, both species offer a unique opportunity to study plant-fungal interactions at the genomic level. Michael G. Muszynski, 2011

The maize supernumerary B chromosome provides an excellent opportunity to investigate changes in the epigenetic nature of the centromere, as this centromere is found in both functional (associated with the centromere specific histone CENH3) and non-functional states. However, determining the epigenetic status of the centromere core is not trivial, as microarray and deep sequencing approaches have difficulties assessing changes from sequences of highly repetitive DNA. In this paper, immunofluorescence assays are used to determine DNA methylation states on stretched pachytene chromosomes. The authors confirm previous reports that the centromere cores in maize, rice and Arabidopsis are typically hypomethylated and associated with CENH3, distinguishing this functional region from the neighboring pericentromeric regions. Using a translocation line with an inactivated B centromere, Koo et al have demonstrated that the inactivated centromere core in this line is associated with DNA hypermethylation. This result suggests that the epigenetic modification of DNA methylation is associated with centromere function and activity. However, it remains unknown if this DNA methylation effect is a cause or consequence of centromere inactivation and CENH3 disassociation. Keith Slotkin, 2011

Many plants have evolved mechanisms to cope with the tradeoffs between carbon dioxide fixation and water loss caused by gas exchange through stomata. One of the most effective mechanisms is C4 photosynthesis, in which carbon dioxide is captured in the mesophyll cells, then diffuses via plasmodesmata to adjacent bundle sheath cells where carbon dioxide is released near the primary carbon fixing enzyme of photosynthesis RuBisCO. A key to this carbon dioxide concentration mechanism is the differentiation of mesophyll and bundle sheath cell identities, which express distinct components of the C4 photosynthesis pathway. C4 photosynthesis has evolved independently from diverse angiosperms that employ C3 photosynthesis. In this paper, Brown et al. demonstrate that bundle sheath specific expression of one C4 pathway enzyme, NAD-dependent malic enzyme (NAD-ME), requires a specific 240 nucleotide sequence found in the 5' end of the transcript. Interestingly, this sequence is conserved in both C3 species (including Arabidopsis and rice) and closely related C4 species (cleome and maize). Furthermore, C4 species show bundle sheath specific expression of NAD-ME, even when the sequence comes from a C3 species so long as the conserved 240-nt region is present. Thus it appears that a conserved post-transcriptional regulatory mechanism has been independently recruited to direct bundle sheath specific expression in C4 species as diverse as maize (a monocot) and cleome (a eudicot). It remains unclear what mechanism is regulating bundle sheath specific expression of NAD-ME, but these results suggest that C3 species already have both enzymes and a conserved but latent regulatory mechanism that can potentially facilitate a shift to C4. Clinton Whipple, 2011

Several of the most important advances in genetics made use of maize kernels containing anthocyanin pigments. For example, studies of spotted kernels led to the discovery of transposons. When these mobile genetic elements jump into or out of a gene required for anthocyanin synthesis, the result is a sector of the kernel with different pigmentation than the rest of the kernel (i.e. a spot). Anthocyanins are a family of purple or red pigments that accumulate in the aleurone layer of maize kernels. The anthocyanin biosynthetic pathway has been studied extensively at the genetic and biochemical levels and is an excellent model for understanding gene regulation. Mutants are available for every step in the pathway, all of the metabolic Intermediates are known and the genes for every step in the pathway have been isolated and characterized, except one. This paper describes the isolation and characterization of the only uncharacterized gene in the anthocyanin biosynthetic pathway. The Pr1 gene encodes a flavonoid 3-hydroxylase (F3H) that catalyzes the conversion of red anthocyanins to purple ones, so kernels lacking Pr1 activity are red. The authors took advantage of the maize genome sequence to identify a putative F3H gene and characterized several mutations in this gene to establish that it is responsible for Pr1 activity. Further, this gene complements an Arabidopsis mutant lacking F3H activity and is regulated by genes known to regulate the anthocyanin biosynthetic pathway. Taken together, these experiments provide convincing evidence that the gene characterized in this paper is Pr1 and constitutes the last step to be characterized at the molecular level of this pathway.

This paper adds to the growing number of genes identified in maize that are critical for axillary meristem initiation. Interestingly, several of these genes are not known from Arabidopsis mutants, including Barren stalk1 (Ba1) and Barren stalk fastigiate1 (Baf1). baf1 mutants fail to produce ears in some genetic backgrounds, and when ears are produced in permissive backgrounds they are fused to the stalk suggesting that Baf1 is involved in both axillary meristem initiation and proper boundary formation. The authors show that Baf1 encodes a protein with an AT-hook DNA binding domain. The AT-hook family is present throughout the land plants, but is poorly characterized functionally. The BAF1 protein appears to be nuclear localized and can homodimerize, suggesting that it functions as a transcription factor. Baf1 is expressed in a narrow stripe of cells adaxial to initiating meristems, in a domain that is identical to Ba1. Interestingly, Baf1 expression in this domain requires Ba1 activity, suggesting that Ba1 and Baf1 act in a common pathway required for meristem initiation. However, baf1 mutants are much less severe that ba1 mutants indicating that other redundant factors are required to promote axillary meristem initiation downstream of Ba1. That orthologous mutants are not known in Arabidopsis demonstrates the utility of maize genetics in spite of high levels of redundancy. It will be interesting to further link Baf1 and Ba1 function with what is known about auxin-mediated axilary meristem initiation. Clinton Whipple 2011

Transposable elements (TEs) can rapidly increase in copy number, generating genome size differences between individuals of the same species, prime examples of which are cotton and rice. Zea luxurians and maize separated ~140,000 years ago, prior to maize domestication. The Z. luxurians genome is ~1.5 fold larger than the maize B73 genome. To determine if this recent evolutionary size difference is due to TE activity, Tenaillon et al used paired-end Illumina sequencing to survey the composition of the maize B73 and Z. luxurians genome. They found that both genomes have roughly ~85% TEs, and the types of different TEs and their relative distribution in the genome are highly conserved. TEs account for 70% of the size difference between the two genomes, with the other 30% of size difference still unaccounted for. The similarity in TE number and distribution is surprising, as TEs are the most dynamic part of the genome and it was expected that one or several TE families would show rapid amplification responsible for the genome size polymorphism. This study demonstrates that short-read deep sequencing can be a powerful tool in accessing the genic and TE composition of a genome. This powerful approach can be used to explore the genome size and TE content changes upon domestication and inbreeding in the maize lineage. Keith Slotkin, 2011

The synthesis and degradation of starch in plant leaves is a dynamic process that follows a daily cycle. During the day (light phase) starch is synthesized from the sucrose produced by photosynthesis and during the night (dark phase) the starch is degraded and used for both metabolism and export to sink organs. In this paper, the authors investigated the role of one of the isoforms of the starch synthesis enzymes, starch branching enzyme IIa (sbe2a), on transitory starch accumulation in leaves. The transitory starch in maize leaves is a branched polymer of glucose units mainly composed of amylopectin. The synthesis of amylopectin requires the action of starch branching enzymes (SBEs), of which, maize has three: SBEIa, SBEIIa and SBEIIb that show differential accumulation in leaves and endosperm. In this work, SBEIIa was shown to be the primary SBE responsible for the production of transitory starch granules in leaves that can be efficiently degraded during the night. In sbe2a mutants, the starch polymer is improperly branched leading to the formation of irregular granules. The authors hypothesize that the abnormally shaped granules are not properly degraded leading to hyperaccumulation of starch in leaves. Either due to the increased accumulation of starch or metabolic changes associated with more starch, sbe2a mutants show premature senescence and many hallmarks of programmed cell death. Thus SBEIIa is required for proper starch granule structure allowing for efficient diurnal cycling of transitory starch in leaves. Mike Muszynski, 2011

doi: 10.1104/pp.111.174094

Plants flower in response to a combination of internal and external cues that regulate production of a mobile floral-promoting signal called florigen. Key experiments in tomato, rice and Arabidopsis in the last several years have produced convincing evidence that proteins with homology to phosphatidylethanolamine binding proteins (PEBPs) encoded by the FLOWERING LOCUS T (FT) gene in Arabidopsis and related genes in other species have florigenic activity. FT-like genes with floral-promoting activity have been identified in a growing number of plant species but, until recently, maize was not counted among them. This is no longer the case. Meng and co-authors have identified one of the 16 maize FT-like genes, called Zea mays CENTRORADIALAS (ZCN), as possessing florigenic activity using a number of experimental criteria. Their systematic approach showed ZCN8 has all the characteristics expected for a florigenic gene. Moreover, their analysis of the floral transition and ZCN8 expression in day-length sensitive tropical lines compared to insensitive temperate lines indicates the diurnal expression of ZCN8 plays a role in how flowering is controlled in response to photoperiod. An illuminating study, indeed! Mike Muszynski, 2011

In this paper the authors take a radical approach to the assembly and ordering of genetic elements in a plant genome. They utilize technically diverse data types to order contigs and sequences in Barley. Flow sorting of chromosomes, next generation sequencing, SNP mapping, classical cytogenetics, and leveraging of other complete genomes in the cereals are used to provide a first pass at he order of genes in Barley. The article was startling not only for the value the research provides for genetic mapping and genome-enabled biology in Barley, but also for the implication that a similar approach (or subset of approaches) coudl be taken to improve the annotations of maize and other cereal genomes. Indeed, the approach could be used to generate a set of testable hypothesis for genome organization in any group of organisms for which multiple co-linear genomes are available. As crop genomics moves forward, the sort of genetic and bioinformatic flexibility shown in this paper may well lead to comparatively improving genome assembly and contig ordering. Brian Dilkes, 2011

I think about grain tissues and proteins in these tissues a lot and I was fairly comfortable with my understanding of the roles of these tissues and proteins until I read this paper. Starchy endosperm provides nutrition to the germinating seedling by accumulating starch and seed storage proteins such as zeins. On germination, the (usually) single cell layer on the outside of the endosperm called the aleurone makes hydrolytic enzymes that degrade these storage compounds to provide energy and metabolites to the germinating seedling. The authors of this paper demonstrate that like starchy endosperm, aleurone cells accumulate seed storage proteins (although at a lower level than starchy endosperm). What are these proteins doing in there? A reasonable explanation proposed by the authors is that they serve as a source of reduced nitrogen and carbon for the synthesis of hydrolytic enzymes by aleurone cells. The cell biology resulting in accumulation of seed storage proteins in aleurone cells is particularly interesting. In starchy endosperm, seed storage proteins accumulate in endplasmic reticulum-derived protein bodies, while in aleurone they accumulate protein storage vacuoles. An elegant set of micrographic experiments involving fluorescently-tagged proteins and antibody markers to subcellular marker proteins suggests that seed storage proteins arrive at aleurone protein storage vacuoles by a novel pathway. This pathway may help explain how the storage proteins of other cereals are deposited. Paul Scott, 2011

The maize and sorghum genomes are both functionally diploid and contain ten chromosomes. However, the maize genome underwent a tetraploidy event sometime after the divergence of the maize and sorghum lineages. Many of the duplicate genes (homeologs) in maize have not been maintained. This gene loss combined with chromosomal rearrangements have created a dynamic maize genome that has winnowed the genes and chromosomes back to the ancestral chromosomal number. Interestingly, the gene loss did not occur equally among the subgenomes produced by the maize tetraploidy event. By comparison of syntenic regions of the maize and sorghum genomes, the authors of this paper show that the process of gene loss has been concentrated in one of the maize subgenomes. Furthermore, presence absence variation for genes in diverse maize and teosinte lines shows that polymorphism for gene loss appears to be more frequent in one genome suggesting that the process of gene loss in maize is ongoing. Finally, the authors show that among duplicate genes that have been maintained there are frequent expression differences among the subgenomes, with the same subgenome that frequently loses genes showing reduced expression levels. They suggest a mechanism whereby deletion rates are equal among both subgenomes, but purifying selection maintains genes from the dominant subgenome that exhibits higher expression. Clinton Whipple, 2011

Angiosperms deliver non-motile sperm cells via the male gametophyte or pollen. Following pollination, sperm cells travel down the growing pollen tube and are only released as the pollen tube comes in contact with the female gametophyte. The synergid cells of the female gametophyte are known to excrete a mobile signal important for the final stages of pollen tube guidance towards the female gametophyte. The authors of this paper show that synergids also produce a signal that is required to both stop pollen tube growth and rupture the tip to release the sperm. A subfamily of four short cysteine-rich defensin-like proteins (ZmES1-4) are expressed in in the embryo sac, particularly in the synergids. Knockdown of these genes by RNAi results in female sterility due to the inability of the pollen tube to release sperm after encountering the female gametophyte. Defensin and defensin-like proteins have diverse functions including anti-fungal or anti-microbial activity in other plants, and as venom components in animals. Unlike other plant defensins, ZmES1-4 has weak anti-microbial activity. However, ZmES4 is sufficient to induce pollen tube bursting by an interaction with KZM1, a potassium channel in the membrane of the pollen tube. The ability of ZmES4 to induce pollen tube rupture appears to be species specific. It remains to be determined if this pathway is conserved in other angiosperms. Clinton Whipple, 2011

The juggernaut continues in the molecular identification of maize auxin pathway genes by the Auxin EvoDevo project. The vt2 gene can now be added to the ever growing list of auxin biosynthesis or signaling genes identified that function in organogenesis in the maize shoot. Unlike Arabidopsis where many auxin pathway genes function redundantly, in maize, mutations in single genes have dramatic impacts on vegetative and reproductive development. vt2 mutants, similar to another auxin biosynthetic mutant sparse inflorescence1 (spi1), have reduced shoot growth and an almost completely barren inflorescence lacking most axillary meristems. The vt2 gene was shown to encode a co-ortholog of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA1), involved in Trp-dependent auxin biosynthesis. Double mutant analysis with spi1 indicated that, unlike previously thought, spi1 and vt2 likely function together in the same auxin biosynthesis pathway. Cloning of vt2 adds another gene to the rapidly expanding maize auxin pathway and adds to our understanding of the evolution of how auxin shapes plant development in different species. Mike Muszynski, 2011

I decided to go with a more applied paper this time. Commercial transgenic maize lines on the market to date address input traits, making maize resistant to insects or herbicides, thereby increasing yield and ease of production. Input traits benefit the public by decreasing the cost of food production, but this benefit is often not readily apparent. This paper demonstrates a transgenic approach to controlling fungal infections which can cause a reduction in yield, so fungal resistance can be considered an input trait as well. However, some fungi produce dangerous toxins so controlling these fungi would improve crop safety. Fungal resistance can therefore be considered an output trait as well, with a direct benefit to the public in the form of increased food safety. The approach taken by these authors exploits a viral gene called KP4 that kills the fungus Ustilago maydis or corn smut. Several transgenic lines were produced that express varying levels of the KP4 transcript and its corresponding protein. Resistance to Ustilago maydis infection correlated with the levels of KP4 transcript and protein in transgenic maize plants inoculated with the fungus. Further, leaf extracts from transgenic plants inhibited the growth of Ustilago maydis in culture. While Ustilago maydis is does not have as large an economic impact as some other fungi, this work is important because it establishes an additional method that can be used in addition to traditional methods such as breeding and improved management practices for control of fungal infections. Paul Scott, 2011

Apomixis is a form of asexual reproduction where meiosis is avoided and an embryo develops without fertilization. To study this process, which could significantly improve current crop breeding practices, Singh et al performed a clever forward genetic screen where only mutant plants that dominantly bypass meiosis produced seeds. Putative mutants were tested by flow cytometry and Dnr4 was identified as a single locus responsible for promoting entry into meiosis. Dnr4 encodes the AGO104 ARGONAUTE protein, which is likely similar to the Arabidopsis AGO9 protein, although there are important differences in the interpretations of their phenotypes as well as their regulation (Olmedo-Monfil et al., 2010 Nature v.464). Dnr4/ago104 mutant plants have reduced CHH and CHG DNA methylation of centromeric repeats, increased expression of these repeats and transposable elements, and a loss of centromeric condensation before entry into meiosis. Together, these data demonstrate that ARGONAUTE proteins, and presumably small RNA pathways, are responsible for regulating chromosome condensation and progression into meiosis. This paper is the latest in a series that demonstrates that in plants, epigenetic regulation, chromatin condensation and small RNA pathways are responsible for the entry into sexual reproduction (Nonomura et al., 2007, Plant Cell v.19)(Olmedo-Monfil et al., 2010 Nature v.464)(Garcia-Aguilar et al., 2010, Plant Cell v.22). Keith Slotkin, 2011

Whole genome duplications have been correlated with diversification in several plant lineages including the grass family Poaceae. The Poaceae duplication is estimated to have occurred about 70 million years ago, before the divergence of the rice and sorghum/maize lineages. In the majority of cases, only one of the duplicate genes has persisted, but in about 17% of the cases a paralogous pair of genes has been maintained. These paralogous genes accumulated independent mutations following the duplication, creating distinct gene lineages. This paper investigates an interesting duplicate region of the grass genome (Rice Chromosomes 11 and 12/Sorghum Chromosomes 5 and 8), in which duplicate pairs have diverged significantly less than would be expected. This similarity appears to be due gene conversion mediated by recombination among the homeologous chromosome pairs. Interestingly, the similarity is graded along the length of the chromosome with the least divergence on the distal arms, and becoming more divergent towards the pericentromeric region, creating "strata" in which the paralogs appear progressively younger as you approach the distal end. Homologous chromosomal regions were identified in maize, although the more recent whole genome duplication and subsequent genomic rearrangements in the maize lineage have obscured the synteny with the more obvious case in rice and sorghum. The authors discuss possible mechanisms by which this unusual duplicate region was created maintained. Clint Whipple, 2011

In another demonstration of genome-enabled biology in maize, the nested association mapping population (NAM) was used to examine leaf architecture. Genes controlling leaf angle, strongly associated with plant density tolerance, as well as leaf length and width were mapped by joint QTL analysis. This approach netted 30, 34 and 46 QTL for the three traits with very little overlap for QTL between traits as ascertained by position estimates and trait correlations. In an effort to further localize QTL and leverage the nested population, 1.6million SNPs were catalogued in the parents of the NAM and the genotypes of each RIL estimated based from the 1100 linkage markers used to construct the genetic maps. This approach leverages information from the parents and projects very high resolution genotype data onto the low recombination density RIL. This allowed the researchers to use the historical recombinations present in the founders and attempt association mapping of traits to particular SNP. The approach was remarkably powerful, identifying a large number of SNPs present within the QTL windows detected by joint mapping. More associations, and greater precision and power, may be possible with yet more markers. Still association analysis detected clusters of significant SNPs associated with QTL positions in more than one case suggesting that QTL detected by linkage analysis may have complex genetic bases. Demonstrating the added value of building and utilizing resources such as NAM in maize, the authors detected major associations with two genes known to affect leaf angle in classical maize genetics studies: liguleless1 and liguleless2. The detection of strong QTL at these loci segregating in cultivated maize, may allow the considerable information about their molecular nature and partners to be harnessed in future improvement. The supplementary data for this manuscript are not to be missed and provide a wealth of information linking SNPs to yield data, genome annotation, and demonstrating the sufficiency of an additive model to explain parental phenotypes when the genotypes at detected QTL are fit to the observed phenotypes. Brian Dilkes, 2011

With the completion of the maize genome we learned that transposable elements occupy a whopping 85% of the total sequence. While only comprising 2.2% of the genome, one of the least understood transposable element types are the Helitron elements. Helitrons are difficult to identify, due to their lack of terminal repeats longer than a few base pairs. Just before the completion of the genome, Yang and Bennetzen performed a computational analysis of Helitron elements in B73. They confirmed previous findings that Helitron elements have a propensity to copy gene sequences into the Helitron element itself. They found that 60% of all Helitrons (1,194 of 2,000 intact elements) have incorporated at least one gene fragment, while some elements have incorporated up to 10 unlinked gene fragments. For example, they found that over 700 elements carry a fragment of a phosphatase 2C-like gene, giving new meaning to the term ???high copy gene family???. Of Helitrons that capture multiple gene fragments, elements in which the gene fragments are oriented in the same direction are more likely to be retained. In addition, some of these elements seem to be undergoing evidence of adaptive selection. Lastly, 9% of Helitrons are represented in EST databases. Although previous findings have independently provided evidence of many of these features, this manuscript provides an understanding of the totality of Helitron family size, location, and gene fragment acquisition in the maize genome. All of these findings together suggest that although Helitron elements only occupy 2% of the genome, their role in the genesis of new genes and new protein functions may be extraordinarily high. R. Keith Slotkin, 2011

Who could resist browsing through an atlas of transcription through maize development? Certainly not I. These authors undertook the yeoman's task of obtaining transcript profiles from 60 different tissue/developmental stage combinations. A data set like this could be approached from many different directions and I was eager to see what direction these authors would choose. The mandatory "overview" information was all there - most of the predicted genes are expressed in at least one tissue and a bunch of them are tissue specific. The large number of tissues and developmental stages sampled allow observation of relationships in expression patterns among tissues and organs as well as gene expression changes that occur in the course of development. The authors focus on expression patterns in leaves and seeds and present detailed results for genes in the lignin biosynthetic pathway. Tissue- and organ- expression patterns of different paralogs of lignin biosynthetic gene yielded some surprising results. This paper reveals the tip of the iceberg in terms of information that can be extracted from this data set, which will soon be released to the community. The data will be a great resource, so get on your favorite database and start mining! Paul Scott

Further, the authors introduce Ac elements conferring varying degrees of transposase activity into the Ds series and observe additional phenotypic variation and transcript level variation. This effect is likely a trans effect on gene expression caused by the binding of the AC transposase to DS elements in the ps1 transcription start region. This effect on gene expression is termed suppression and has been observed in other transposon systems, but not for AC/DS. This work supports a growing body of evidence that transposons have a role in generating the genetic diversity required for evolution and breeding. The observation that a single transposon insertion can change both cis and trans regulation of gene expression has broad implications on the regulation of gene expression because cis regulation is thought to control additive gene effects while trans regulation is thought to control non-additive gene effects such as dominance. These data illustrate that the degree of cis and trans regulation at a given locus can potentially change, presumably changing the gene action of the locus. Hypotheses abound in which a given type of gene action is thought to be responsible for such important phenomena as heterosis or inbreeding depression and these hypotheses should be evaluated in light of these results. Paul Scott, 2011

This is an interesting paper because it provides examples of a transposon system influencing gene expression through two different mechanisms. The gene under investigation is Ps1, a gene that is essential for carotenoid biosynthesis. Mutants with reduced function of this gene accumulate metabolic intermediates that cause the scutellum to be pink while severe mutants are lethal. Transcription of this gene is unusual because it lacks the TATA and CAAT sequences that facilitate transcription initiation in many genes. One consequence of this is that the transcription start site of this gene varies widely for different transcripts. The authors used a transposon-induced mutation containing an AC transposable element in the area in which transcription normally starts to produce a series of DS elements in this area. Phenotypic severity varies within this series as do transcription start sites, indicating the transposon insertions have a cis effect on expression of ps1.

It has long been hypothesized that transcription factors are more likely involved in morphological evolution than other genes. While this hypothesis is consistent with the majority of developmental mutants and many of the genes underlying QTL, it has not really been tested systematically. In this paper that authors investigate a single family of transcription factors, the MADS-box genes which are known to play diverse roles in the development of plants. Specifically they sequenced 32 MADS-box genes, representing all known Type-II MIKC type MADS-box in maize, from a diverse set of maize and teosinte lines. This was compared with a control set of 32 randomly chosen maize genes. Selection tests clearly showed that more MADS-box genes were under selection during maize domestication or improvement than the randomly chosen set, and this enrichment of selected MADS-box genes was statistically significant. While it is not known if other transcription factor families show a similar enrichment, it is now clear that MADS-box genes are not only key developmental regulators, but they also have played a role in the domestication of maize. It is likely that this selection for MADS-box alleles mediated some of the dramatic morphological evolution that occurred during maize domestication, and future work will be necessary to uncover exactly what their roles have been. Clint Whipple, 2011

The regulation of transposable elements (TEs) through the lifecycle of an individual is not static, but rather a dynamic process between the TE and host organism. In maize, Li et al have found that the levels of LBL1/SGS3 in leaves affect freshly silenced MuDR TEs during the transition from juvenile to reproductive growth. LBL1 regulation itself is a key component in the tasiRNA-induced phase change, and the affect of LBL1 regulation is manifested on the MuDR TE as reduced DNA methylation, reduced repressive histone modifications, and transient expression. In addition, in cg1 mutants that prolong developmental phase change, efficient TE silencing is also delayed. Together, this data demonstrates that there is crosstalk between the different small RNA pathways that regulate developmental timing and TE silencing. Keith Slotkin, 2011

The regulation of the timing of phase change, the shift from vegetative to adult growth, has been shown to require the opposing activities of two small RNAs, miR156 and miR172. In turn, each miRNA represses the expression of a subset of two types of plant-specific transcription factor, SPB and AP2-like, respectively. In this report, the authors connect vegetative phase change to another small RNA pathway and to epigenetic silencing of transposons. The authors show that phase change and silencing of the MuDR transposon are associated with reduced expression of leaf bladeless1 (lbl1) and an increase in the levels of the trans-acting small interfering RNA (tasiRNA) target arf3a. They demonstrate that there is a transient loss of lbl1 expression in transitional leaves which they suggest causes coordinated changes in both MuDR silencing and the tasiRNA silencing pathway. The authors suggest this coordination offers plants an opportunity to monitor and silence the potentially dangerous proliferation of transposons as they prepares to enter their reproductive phase of growth. Mike Muszynski, 2011

The Phenylpropanoid pathway leads to important plant metabolites such as anthocyanins and flavonols. Recent interest in biofuels has caused tremendous interest in the phenylpropanoid product lignin. The brown midrib genes have been studied for many years because they alter lignin content and structure and can improve the digestibility of ruminant feed. Brown midrib genes characterized thus far encode enzymes in the phenylpropanoid pathway. In spite of years of study, little is known about genes that regulate the phenylpropanoid pathway. This paper demonstrates that a myb transcription factor binds to the promoter of a phenylpropanoid pathway gene and adds to a growing body of evidence that the R2R3 family of MYB genes is involved in regulating this pathway. Paul Scott, 2011

The pinnacle of epigenetic phenomena is paramutation, where an active allele of a gene becomes epigenetically silenced and is then able to induce the silencing of additional active alleles in subsequent generations. At the b1 gene of maize, the highly expressing B-I allele is identical to the silenced B??? allele with the exception of the epigenetic state of a set of tandem repeats, which are essential for paramutation, way upstream of the b1 coding region. Taking a biochemical approach to studying the b1 tandem repeats, Brzeska et al have identified a protein, which they have named CBBP, that binds the repeats in vitro and in vivo. Most interestingly, constitutively high levels of CBBP protein induced by transgene expression can initiate the conversion of B-I to a B???-like silenced state referred to as B*. Once induced by CBBP over expression, B* can paramutate new B-I alleles without the presence of the CBBP transgene. This paper represents an important step in understanding how paramutation occurs, focusing on steps independent of the RNA-directed DNA methylation pathway. Interesting models of how the plant-specific CBBP DNA binding protein facilitates heritable epigenetic programming of the b1 repeats are discussed. R Keith Slotkin, 2010.

The bladekiller1 (bk1) mutation of maize is defective in shoot apical meristem maintenance, resulting in plants that produce progressively smaller leaves and ultimately abortion of the apical meristem. The authors show that bk1 is caused by loss of function in a thiamine biosynthesis gene (thi2), and mutant plants are rescued by exogenous application of thiamine. Interestingly although thi1, a close paralog of thi2, is present in maize it is not sufficient to rescue the meristem defect, suggesting that thiamine production has subfunctionalized. It remains unclear why maize thiamine biosynthesis would be developmentally partitioned by a gene duplication event. Expression of Thi1 and Thi2 are consistent with a model in which thiamine is synthesized in the leaf primordia and translocated into the shoot apical meristem where it is essential for meristem maintenance and function. Clint Whipple 2011

Dominant dwarfing mutations within DELLA proteins have been responsible for increasing yields through alteration of the harvest index in many crops and thus ushering in the "green revolution". The dwarf plant8 (d8) gene is one such protein and the authors describe the isolation and functional characterization of the dwarf plant9 (d9) gene, the paralog of d8. Although only one dominant, dwarfing D9 allele is described (D9-1), this allele was confirmed as causing alterations to plant stature and flowering time by using transformation of maize and Arabidopsis with both functional and dominant-dwarfing versions of d8 and d9. Interestingly, the D9-1 allele differs from normal d9 by a number of missense mutations and a small indel mutation. The causative polymorphism was localized to the C-terminal E600K mutation through analysis of a comprehensive domain swapping study. Most dominant DELLA mutations affect the N-terminal DELLA or VHYNP domains but the E600K mutation is located in the GRAS domain. Dominant dwarfing mutations in the GRAS domain are rare and are thought function by preventing strong interactions with the F-box SLY1 protein required for degradation by the 26S proteasome. Mike Muszynski, 2011

Working in our summer nursery a couple of weeks ago, I noticed that the plants were a little dry, so I turned on the drip irrigation for the night and went home. I woke up in the early hours of the morning to a loud thunderstorm with a lot of wind. When I arrived at my field the next day, my worries were confirmed as most of the corn had been knocked flat during the night. I knew that the stalks will eventually recover, and I have watched them gradually return to an upright position. I had not given much thought to how maize plants manage this fortunate recovery until reading this paper. Lodging is a source of significant yield losses, not just for maize but also other cereals. Zhang et al. investigate how differential growth of pulvini, the bulbous region at the nodes of the stalk, respond to gravity and return the plant to an upright posture. The pulvini of nodes 9-12 respond to gravity by differentially elongating their cells, with more elongation in the lower region of the pulvinis, which then pushes the stem back towards the sky. This paper takes a detailed look at changes in upper and lower pulvini regions in response to gravistimulation. This includes an analysis of cell wall composition, hormone content, as well as transcript and metabolite profiles. The authors found siginificant changes in cell wall components, particularly lignin, heteroxylan, xyloglucan and heteromannan. They also found significant changes in the levels of the hormones auxin, GA and ABA. These changes were corroborated by the transcriptome and metabolome profiles. The implication of auxin is perhaps not surprising since it is classically known to regulate differential growth in response to environmental stimulation. Interestingly maize mutants like baf1, fail to make analogous pulvini in the tassel, where they function to increase the angle of tassel branches. It would be interesting to investigate pulvinus response to gravistimulation in baf1 and other known maize auxin mutants. Clint Whipple, 2011

The large size of the maize leaf and the presence of a continuous, longitudinal developmental gradient make it an ideal subject for developmental studies. In this data-rich, multi-institutional effort, the authors present a foundation for a systems approach to understanding photosynthetic development. mRNA-seq was used for deep transcriptome surveys in four segments of a seedling leaf, chosen to capture a range of anatomical and biochemical states during development, and in two differentiated C4-related cell types. Expression of 25,800 genes (about 80% of the maize transcriptome) was documented from more than 120 million reads mapped to the genome, including some 80 million from the four tissue zones and 40 million from laser-capture dissected bundle sheath and mesophyll cells. Several visualization tools, including an electronic fluorescent pictograph browser and a 2-cell pathway viewer, are used to display and interpret data analysis, and establish regulatory and biochemical frameworks for photosynthesis. In addition to rich detail about specific gene expression dynamics relevant to C4 photosynthetic development, the study reveals general features of the maize transcriptome that will contribute substantially to ongoing genome annotation efforts. For example, of 20,999 intron-containing genes with detected expression, 9,492 or roughly half showed developmentally regulated, alternative splice forms; about 9,200 of the alternatively spliced genes were newly identified. Alternative splice forms derived primarily from intron retention (60.1%) and exon skipping (32.0%, much higher than from previous estimates). Erik Vollbrecht, 2010

The authors used the Illumina platform to resequence six inbred lines of maize, including Mo17 and five elite Chinese inbreds. Comparison to the B73 sequence revealed considerable polymorphism affecting gene function, including ~2500 premature stop codons, ~800 disrupted splice sites, ~300 frame-shifts, and ~100 altered initiation sites. More evidence for the importance of presence-absence variants (PAVs) was also found, in that 296 high-confidence B73 genes were absent in at least one of the six inbreds, and 570 genes present in the one or more of these inbreds were absent from the B73 sequence. However, resequencing B73 revealed that about two-thirds of these 570 genes are actually present in B73 but not captured by the current genome release! Pat Brown, 2010

Apomixis refers to a broad range of mechanisms that result in the production of progeny that bypass sexual reproduction and, therefore, have the identical genetic composition as their parent. Surprisingly, the RNA-directed DNA methylation (RdDM) pathway, which is responsible for epigenetically silencing transposable elements, has a role in repressing apomixis in both the male and female germ lineages. Garcia-Aguilar et al have demonstrated that maize de novo DNA methyltransferases play a role in repressing asexual reproduction, perhaps in the similar pathway as AGO9 in Arabidopsis (Olmedo-Monfil et al., Nature, 2010). Reproductive cells mutant for the de novo DNA methyltransferases display a transcriptionally active chromatin state, suggesting that a genome-wide and RdDM-induced de novo DNA methylation event occurs during reproductive development. How the de novo DNA methyltransferases and the RdDM pathway act to repress asexual reproduction is currently an enigma, and it will be exciting in the coming years to understand this mechanism. R. Keith Slotkin, 2010.

High throughput genotyping methods have been developed for maize but to fully understand the genotype to phenotype relationship (for QTL, NAM etc), high throughput, accurate phenotyping methods are critically needed. The maize root system in particular is a challenge to phenotype. Tracshel et al have developed a high throughput method to analyze root system architecture in maize grown to maturity in the field. Called ???shovelomics??? (brilliant), the method collects a soil core from beneath a mature plant and measures 10 root architecture traits in less than 10 mins. Paula McSteen 2010

The authors adapted a linear interpolation method for genotype imputation and tested it by attempting to impute data for ~500,000 SNPs in each of the 5,000 NAM lines, which required use of four existing datasets: 1) parental genotypes for the 26 NAM founders for the 500,000 SNPs; 2) parent and progeny data for a scaffold of 1,106 SNPs; 3) the linkage map based on these 1,106 SNPs; and 4) the AGP2 physical map assembly for B73. Data were imputed for all but ~10% of the 500,000 SNPs, which were omitted due to any of four various conditions. For the ~450,000 SNP for which imputation was conducted, genotypes could be "assigned" 73.3% of the time, summed across the 26 populations and including both low (4.6%) and high (68.7%) confidence assignments. This adds about 1.6 billion data points of informative content to the NAM genotype dataset. The dataset that includes both the imputed data and the data from the 1,106 initial SNPs could be called "impuNAM1" and served by MaizeGDB, with subsequent numbered updates provided as new are added to the NAM dataset. Also of interest, the authors document many cases where the NAM and AGP2 data are in conflict with each other, including both discrepancies and eight BACs with known genetic locations that have remained on "Chromosome 0" in AGP2. Nick Lauter, 2010

This paper reports on an economical analysis of the impact of using genetically modified maize plants (Bt maize). Based on large-scale and long-term data sets (~14 years in five states), the authors suggest that farmers planting non-Bt maize near Bt maize get the benefit of a high proportion of the European corn borer (Ostrinia nubilalis) pest control (the so called "hallo effect") that results on cumulative benefits ranging from $1.9 to $2.4 billion; and on the other hand non-Bt maize plants serve as a reservoir of natural populations that potentially delay the evolution of pest resistance (the so called "refuge strategy"). Interestingly, it was highlighted in Nature news that "5 of the 18 authors listed on the paper, work for big food or agri-business companies, including Syngenta Seeds and General Mills". However, the first author stated that authors who work for industry were not involved in the financial calculations. Mario Artega-Vazquez, 2010

McLamore et al have developed a microsensor to non-invasively measure auxin transport in real-time in the epidermis of maize roots. To test the technique, they compared the results from normal roots to the roots of the brachytic2 (br2) auxin transport mutant. As expected, the microsensor was able to detect a reduction of auxin transport in br2 roots. The most exciting result though, is that the technique convincingly demonstrated oscillatory waves of auxin transport in normal and br2 roots with differences in the amplitude and period in br2 roots. Although previous papers had suggested oscillations of auxin flux, this technique is the first to measure these oscillations in real time, opening up a new field in the study of auxin transport in all plants. Paula McSteen, 2010

Many future efforts to identify functional polymorphisms underlying traits of interest are expected to combine aspects of both QTL/linkage mapping and LD/association mapping. One current incarnation of this approach is the NAM population of maize RILs, which was created by crossing 26 inbreds to a single reference parent and obtaining high-density genotypes from the parents and low-density genotypes from the RILs. In this study, the authors use simulation to investigate the power and precision of NAM-like populations to identify functional polymorphisms under many different scenarios, including allelic series (multiple functional polymorphisms in the same genomic region) and mating designs that include multiple reference parents. Pat Brown, 2010

The authors report and analyze a crystal structure for the gene product of vivaparous14 (vp14), a 9-cis-epoxycarotenoid dioxygenase (NCED). VP14 catalyzes the rate-limiting step in biosynthesis of the phytohormone ABA. The structure was solved as a free enzyme but provides various insights into VP14 function including the basis of its interaction with the thylakoid membrane and a model for the interaction of the enzyme's active site with its substrate. In addition to direct insights into ABA metabolism, the structure is a prototype template for other members of the broadly defined family of bacterial, plant and animal enzymes called carotenoid cleavage dioxygenases (CCDs). For example, plant CCDs are involved in production of a variety of signaling molecules including strigolactones. The notion of using VP14 as a structural template for other plant CCDs was tested first computationally and then experimentally by homology modeling of the maize CCD1 protein, which has a commercially available substrate. Sites in CCD1 were selected based on hypothesized structural homology and then mutagenized. When activity was assayed in vitro, mutations behaved as predicted by the homology model. Thus, the structural model of VP14 presents myriad possibilities for altering crops and designing novel chemical agents. Erik Volbrecht, 2010

These two studies from rice demonstrate clearly a close relationship between plant architecture and yield potential in the grasses, through effects on both vegetative shoot and inflorescence architecture. Each group started with a rice line that showed natural variation of both reduced tiller number and increased panicle branching. In map-based cloning efforts with the two different varieties, these cosegregating architecture traits mapped to the same, single locus, OsSPL14, which encodes a SQUAMOSA promoter-binding-like (SPL) protein. Increased expression levels of the OsSPL14 mRNA conveyed both a reduced number of stronger tillers and an increased number of panicle branches and most importantly, increased grain yield. Interestingly, the natural variants alter expression levels in different ways: in one allele OsSPL14 levels are increased due to a point mutation in a miR156 binding site within the OsSPL14 coding region, while in the other allele the causal site maps to un upstream promoter region. Erik Vollbrecht, 2010

The maize leaf epidermis comprises about one third of the cells in leaves and has nearly 20 specialized cell types. As the outermost layer, the epidermis is largely responsible for mitigation of both biotic and abiotic stresses. OCL1 is a member of a large family of HD-ZIP-IV proteins that typically are specific to the epidermis. Thus, investigation of OCL1 function presents a unique opportunity to gain insights into the molecular regulation of epidermis-specific processes. The authors used a 59K long-oligo array to identify at least 35 genes differentially expressed in plants with transgenic overexpression of OCL1 as compared to WT, and confirmed eleven of these by qRT-PCR. This short list functionally connects OCL1 function with lipid metabolism and cuticle biosynthesis, as well as with transport and defense processes. The wax regulatory roles were phenotypically confirmed by characterizing the biochemical differences in epicuticular wax between WT and OCL-OE plants. In addition, the mRNA expression patterns of Ocl1 and these target genes were assessed throughout maize development and showed a high degree of coexpression. Evidence for direct regulation of several of the target genes was obtained by transient promoter-reporter assays. Finally, investigation of mRNA expression of these genes in epidermal and mesophyll tissues of WT leaves by LCM-qRT-PCR revealed a mixture of tissue specific expression patterns. These detailed molecular characterizations have significantly expanded the list of molecular entry points for further investigations of epidermal biology. Nick Lauter, 2010

The authors made cDNA from wild-type and ra3 maize inflorescences, digested with either NlaIII or DpnII, and used the Illumina platform to sequence the resulting fragments between the poly-A tail and the 3'-most restriction site. About 13% of reads could not be mapped, and likely represent B73 sequences not captured by the current reference genome, although a few may result from sequences specific to the ra3 introgression (backcrossed into B73 5 times). Most genes were represented by multiple sequences in a given library, which could represent either incomplete digestion or real variation in polyadenylation/splice sites. A surprisingly high level of antisense transcript production was also observed. 72% of genes differentially-expressed genes between wild-type and ra3 were upregulated in the ra3 mutant. Pat Brown, 2010

These two studies from rice demonstrate clearly a close relationship between plant architecture and yield potential in the grasses, through effects on both vegetative shoot and inflorescence architecture. Each group started with a rice line that showed natural variation of both reduced tiller number and increased panicle branching. In map-based cloning efforts with the two different varieties, these cosegregating architecture traits mapped to the same, single locus, OsSPL14, which encodes a SQUAMOSA promoter-binding-like (SPL) protein. Increased expression levels of the OsSPL14 mRNA conveyed both a reduced number of stronger tillers and an increased number of panicle branches and most importantly, increased grain yield. Interestingly, the natural variants alter expression levels in different ways: in one allele OsSPL14 levels are increased due to a point mutation in a miR156 binding site within the OsSPL14 coding region, while in the other allele the causal site maps to un upstream promoter region. Erik Vollbrecht, 2010

This study reports on the role of different epigenetic modifications associated with paramutation at the b1 locus in maize. This is a very detailed analysis of DNA methylation, nucleosome occupancy and histone modifications at diverse relevant regions, including the key sequences (hepta-repeat) absolutely required for paramutation, showing that nucleosome occupancy and histone modifications are mainly involved in the tissue-specific control exerted by the hepta-repeat while DNA methylation at the hepta-repeat is hypothesized to be an epigenetic mark that define the mitotically and possibly also the meiotically transcriptionally silent paramutagenic state. Mario Arteaga-Vazquez, 2010

This is a very nice paper that provides molecular evidence for a mechanism by which an axillary meristem can acquire a determinate fate and result in the formation of a pair of spikelets. This paper reports on the discovery of the Ramosa1 Enhancer Locus 2 (REL2) as a genetic enhancer of the ramosa1 and ramosa2 mutants and the identification of an intragenic enhancer of the ramosa1 mutant (ra1-RSenh). REL2 encodes a homolog of the transcriptional co-repressor TOPLESS of Arabidopsis. REL2 is capable of rescuing the embryonic defects of a temperature-sensitive TOPLESS mutant and it also shows transcriptional repressing activity in Arabidopsis. The mutation in ra1-RSenh(intragenic enhancer) at the conserved EAR-like repressor motif suggested that a transcriptional repressor mechanism is involved in the establishment of spikelet-pair meristem determinacy. This prompted the authors to test and to confirm that the transcriptional co-repressor REL2 and RA1 physically interact. The authors propose a model for maize spikelet-pair meristem determinacy in which RA1recruits REL2 to the promoter of its target genes (yet to be discovered) via an interaction involving two EAR repressor motifs and the CTLH domain of the REL2 protein. Mario A. Arteaga-Vazquez, 2010

B chromosomes in maize have been exploited historically as tools for genetic studies including a recent emergence as a basis for construction of artificial chromosomes. Much of their utility is based on the contrasting mitotic stability of the B chromosomes in the diploid sporophyte plant, and relatively predictable instability in the male gametophyte or pollen grain. The B centromere tends to nondisjoin (NDJ) in the second pollen mitosis. This study uses FISH technology to examine B chromosome stability in root tip mitoses. At low copy number, B chromosome NDJ was basically absent, while NDJ increased with increasing numbers of Bs. Moreover, B chromosome gain due to NDJ rates was more frequent in plants with even-numbered than odd-numbered B copy number. The disparity is surprising given that homologs do not pair in mitosis. Overall these results demonstrate that the capacity of the B to undergo NDJ is not restricted to the gametophyte. If the observations are also true for other sporophytic tissues, the data raise the possibility of harnessing NDJ to manipulate B copy number in a variety of plant tissues. Erik Vollbrecht, 2010

Plants use an internal clock to anticipate and respond to both diurnal and seasonal changes in the environment. Using RNA harvested from B73 seedlings every 4 hours in conditions of constant light and temperature, an Affymetrix array, and two different algorithms to detect rhythmic expression, the authors estimate that approximately 10% of the maize transcriptome is under circadian control. Pat Brown, 2010

Repeat subtraction-mediated sequence capture (RSSC) was previously developed by human genome researchers and has now been shown to work effectively for maize. This is an important breakthrough for sequencing or resequencing targeted regions of genomes including the "non-repetitive" fraction of model genomes based upon reference sequences, or of non-model genomes after minimal investment in skim-sequencing to define the repetitive fraction. For model species with large and/or repetitive genomes, this technology has broad application potential; It will be useful to maize researchers for defining candidate polymorphisms in regions known to harbor QTL, for allele mining at genes of interest, and for population genetic studies. Nick Lauter, 2010

Similar to what was observed for arabidopsis, the authors clearly demonstrate that biased fractionation has occurred in the maize genome following the most recent tetraploidization event. This preferential removal of genes from one of the ancestral diploid genomes was revealed through comparison to Sorghum, which shared a common ancestor with maize directly prior to the tetraploidization event. It is shown that the missing genes were actually lost, rather than translocated, and that the gene losses have largely occurred via many small events, rather than in blocks. Illegitimate recombination is suspected as a mechanism for initial disruption and removal events, evidenced by presence of direct repeats in carefully studied examples of disruptions. Careful investigations of how else the remnant ancestral diploid genomes might be distinguished were performed, finding that both recombination and nucleotide substitution rates were similar. Also, a preliminary investigation of methylation levels failed to show a clear correlation. Although there are as yet no smoking guns, an epigenetic mechanism for distinguishing between the two diploid genomes newly present in the tetraploid is proposed to explain the source of the bias. Nick Lauter, 2010

This paper contains insights into the molecular basis of paramutation at the b1 locus in maize. Paramutation is an interaction between alleles that leads to the heritable change of expression of one of the alleles. This paper shows that the tandem repeats involved in paramutation at the b1 locus in maize are most likely transcribed by RNA polymerase II and short interfering RNAs (siRNAs) are produced from the b1 tandem repeats. siRNA content does not allow to distinguish between alleles involved in paramutation (B-I and B') and neutral alleles (b), not involved in paramutation in the tissues examined. However, when b1 tandem repeats siRNAs are produced from a transgene expressing a hairpin RNA, b1 paramutation can be recapitulated. It is hypothesized that either b1 tandem repeats siRNAs or the dsRNA template mediates the trans-communication between alleles that establishes paramutation. As a side story, there is supporting evidence for a role for the mop1 gene in the biogenesis of a subset of microRNAs. Mario Arteaga-Vazquez, 2010

This study compares the results of QTL mapping for grain yield in two maize populations with the same parents. The only difference between the populations is that one was intermated for several generations and the other was not. However, fewer than 50% of the QTLs detected were shared between the two populations. In some cases a single QTL in the conventional population was split into 2 QTL in the intermated population. Also, QTL in the intermated population generally explained less variance. This suggests that conventional QTL may often represent stacks of linked QTL. Fewer QTL were detected overall in the intermated population, likely because the effect sizes of individual QTL were smaller than those of stacked QTL. These results suggest that inferences about the genetic architecture of a trait depend considerably on the types of populations evaluated. Pat Brown, 2010

This paper shows very interesting data regarding UV-B (8 h treatment) induced epigenetic changes including, increase in histone H3 acetylation and decrease in DNA and H3K9me2 methylation (interestingly, no changes in siRNA levels were detected) that correlate with activation of Mutator transposons (measured as an increased in transcript abundance). Mario A. Arteaga-Vazquez, 2010

Published in the journal Epigenetics.

The recessively inherited ragged seedling2-Ref mutation conditions defects in mediolateral leaf development, such that leaves become cylindrical. However they are not radially symmetric in cross section. Thus, rgd2-Ref mutants have problems in establishing midrib-to-margin gradients in primordial leaves, but not central-to-peripheral gradients in the shoot apex. The overlap between the mechanisms that establish these gradients is intricate and difficult to tease apart. Toward this end, the authors cloned ragged seedling2 by finemapping the rgd2-Ref mutation and then developing and testing candidate gene hypotheses based on known gene functions. rgd2 was shown to encode an AGO7-like protein that, like AGO7, is required for biogenesis and regulation of trans-acting small RNAs that antagonize auxin response factor transcripts. Rgd2 transcript was shown to be expressed on both the adaxial and abaxial sides of plastochrons 0 and 1, which differs from how AGO7 and the rice ortholog are expressed. This pattern is consistent with rgd2-Ref mutant plants still possessing both abaxial and adaxial tissue identities. Additionally, the authors showed that RGD2 is required for proper localization of miR390, which also plays a role in establishing mediolateral gradients for normal leaf development. In rgd2-Ref mutants, miR390 overaccumulates in the SAM compared to wildtype. Together, these new results provide key entry points in determining how these developmental pathways act differently in monocot versus dicot leaves. Nick Lauter, 2010

Heterosis for grain yield drives the maize hybrid seed industry, but the accurate prediction of heterotic responses using parental phenotypes and genotypes has proven elusive to maize breeders. In this paper the authors phenotype 17 traits in ~300 diverse hybrids and show that heterosis is observed for nearly all traits, although it is strongest for yield. Prediction of hybrid phenotypes from parental phenotypes is most accurate for flowering time and least accurate for yield. The effect of genetic distance on trait heterosis is usually significant but the proportion of variance explained is generally very small. Significant correlations between heterotic responses were observed for several traits including total yield, kernel weight, and cob length. Because total grain yield is a very complex integrated response to variation in a number of traits, the authors suggest that we may improve our understanding of heterotic mechanisms by studying specific yield components. Pat Brown, 2010

Comments: These two papers demonstrate that double-stranded duplex of endogenous and exogenous short interfering RNAs (siRNAs) in plants act as mobile silencing signals between plant cells and can direct epigenetic modification. This is a great contribution to the field. Early this year, it was demonstrated that microRNAs (miRNAs) are also mobile signals that can control gene expression during plant development. Mario Arteaga, 2010

Comments: These two papers demonstrate that double-stranded duplex of endogenous and exogenous short interfering RNAs (siRNAs) in plants act as mobile silencing signals between plant cells and can direct epigenetic modification. This is a great contribution to the field. Early this year, it was demonstrated that microRNAs (miRNAs) are also mobile signals that can control gene expression during plant development. Mario Arteaga, 2010

This paper, dedicated to the memory of maize geneticist and senior author Evgueni V. Ananiev, analyzes six maize genes having the closest phylogenetic relationship to Arabidopsis TERMINAL FLOWER1. TFL1 and the homologous gene FT integrate the floral transition pathway in Arabidopsis, in part by acting as mobile signals. Of 25 TFL-related genes from maize, ZCN1-6 are examined here by constitutive overexpression in transgenic maize. Each has a unique phenotype but trends emerge. For four genes, overexpression led to dramatically delayed flowering, ~1 to 2 weeks in the conditions of this work. Delayed flowering phenotypes correlated with increased branching in the tassel, supporting the notion that basal branches in the tassel (and therefore control of branch meristem determinacy) are regulated in association with the transition period between vegetative and floral phases. This finding is similar to that of many TFL-homolog overexpression studies in dicots, which is interesting given that many components of the genetic networks regulating inflorescence architecture in the grasses are simply not present in dicot inflorescences studied to date. Thus, the ZCN loci may have a conserved role in regulating more fundamental signals such as plant hormones. The paper also includes nice in situ expression studies that identify tissue-specific domains in developing vasculature and at the base of lateral meristems in the inflorescences and vegetative shoot. Erik Vollbrecht, 2010

Chintamanani et al identified and characterized Hrml1, the Hypersensitive Response-modulating locus1 using a clever QTL mapping approach. The partially dominant autoactive disease resistance gene, Rp1-D21, which causes HR lesions to form spontaneously, was crossed onto each IBMRIL in order to map B73 versus Mo17 allelic differences that affect the hypersensitive response. At Hrml1, The B73 allele strongly suppresses HR relative to the Mo17 allele. Allelic variation at the same locus was demonstrated for additional allelic contrasts as well. Additional minor effect QTL affecting HR modulation were also detected. By example, this paper describes a useful method for unveiling subtle genetic variation that may otherwise remain phenotypically cryptic. "Mutant-assisted gene identification and characterization" uses parallel test crosses to create novel phenotypic contexts in which to experimentally assess genetic effects using existing research populations. After one generation of breeding, analysis can be performed with no further genotyping required. One caveat is that the dominant mutation should be donated by a true breeding plant, although an advanced backcross donor could also be used, depending on the phenotype. With current access to doubled haploidization, generation of an optimal true breeding donor line is rapid and inexpensive, making the "mutant assisted" approach to quantitative trait dissection even more accessible for rapid discovery and characterization of minor-effect QTL alleles, particularly those that may be rare and otherwise difficult to stumble across. Nick Lauter, 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.

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 authors characterize five tassel sheath mutants and show that Tsh1 encodes a GATA zinc-finger protein homologous toHAN of Arabidopsis. They then show that the bract suppression function of Tsh1 is conserved throughout the grass family, but not with Arabidopsis, supporting the hypothesis that suppression of bract growth has evolved multiple times through independent mechanisms. Nick Lauter, 2010

The fungus, Ustilago maydis, induces tumors on maize tissues resulting in corn smut disease.Walbot and Skibbe (2010) showed that both vegetative and reproductive organs in maize produced tumors upon Ustilago infection, but which organs produced tumors depended on the stage of development when the plant was infected. This is because Ustilago can only form tumors in tissues that are actively dividing. Skibbe et al (2010) performed comprehensive expression profiling experiments of both maize and Ustilago genes altered in expression in response to infection of maize at different stages of development. Surprisingly, they found that the genes induced or repressed in either maize or Ustilago differed depending on the organ type. They propose that although some common genes maybe required for initial infection, the ability of the fungus to subvert the development of a particular organ requires specific genes in the fungus and in the host. Paula McSteen, 2010

This paper reports the systematic identification of putative maize orthologs of the tomato fw2.2 gene which is thought to be a negative regulator of cell number and governs a quantitative trait locus involved in determining fruit weight. The authors identified 13 members of the so called Cell Number Regulator gene family and show a very detailed expression pattern of several family members in different tissues (by MPSS and RT-PCR analysis). Using a transgenic approach, the authors show that transgenic overexpression of CNR1 reduces plant and organ size while downregulation of the gene correlates with enhanced plant growth, supporting the idea of CNR1 playing a role as negative regulator of cell number. Mario Arteaga, 2010

McClintock's discovery of the Ac/Ds transposable element system involved extensive studies with so-called state I Ds elements, which cause chromosome breaks in the presence of Ac. This paper uses an elegant combination of classical, cyto- and molecular genetics to elucidate the mechanism underlying this process that can potentially reshape genomes over evolutionary time. It has been known for several years that the crux of Ac/Ds chromosome breaking activity is so-called alternative transposition due to the relatively close physical association of multiple intact or fragmented Ac/Ds elements. Essentially, the transposase 'gets confused' and uses one transposon end from each of two different full or partial elements. Among a variety of element arrangements and potential end pairs, this study queries the specific rules that govern chromosome breakage. The authors generate new transposon alleles of the p gene, each involving an intact Ac (with two ends) and a fractured Ac (with one end), and using them show that breakage occurs when the extra end does not match both the identity (5' or 3') and orientation of its nearest Ac end. On the other hand, a matched extra end may result in macrotransposon activity but does not induce state I-type breaks. Importantly, these data clearly separate the macrotransposon and breakage outcomes of alternative transposition. Furthermore, breakage frequency correlates inversely with the distance between two unmatched ends, analyzed for a range of separation from approximately 0.8-15 kb. Cytogenetic studies of meiocytes confirm that breakage occurs following transposon-induced fusion of sister chromatids, as predicted by the alternative transposition model. Erik Vollbrecht, 2010

Liu et al describe a great new method for using bulked segregant analysis (BSA) to map maize mutants. The original method of BSA mapping described by Michelmore et al 1991 was to use Restriction Fragment Length Polymorphism (RFLP) or Random Amplified Polymorphic DNA (RAPD) markers on a pool of mutant and a pool of non-mutant individuals from a segregating family. Enrichment of linked markers in the mutant versus the non-mutant pool enabled mutants to be assigned to a chromosomal map location. More recently, Simple Sequence Repeat (SSR) PCR primers have been used for BSA mapping which requires about 100 SSR markers to map a mutant to a chromosome bin. In this new method of BSA mapping, 1016 Single Nucleotide Polymorphism (SNP) markers dispersed throughout the genome are assayed on pools of mutant and non-mutant individuals using Sequenom MASSarray mass spectroscopy technology, which enables quantitative detection of SNPs. To demonstrate proof-of-concept of the method, Liu et al mapped 45 out of 49 mutants from several different genetic backgrounds. This method is fast, has high resolution and will greatly facilitate the positional cloning of maize genes. Paula McSteen, 2010

The authors provide the first concrete evidence for gene conversion in maize centromeres. Using transposon display of a centromeric repeat (CRM2) to score 238 markers across 93 IBM RILs, they identify two clear conversion events. Over half of the CRM2 markers (and one of the two markers showing gene conversion) are precipitated with anti-CENH3 antibodies, demonstrating that they belong to functional centromeres. To assess the prevalence and importance of gene conversion over evolutionary time, the authors scored 75 CRM2 markers from all 10 maize centromeres in a panel of 53 diverse maize inbreds. Re-genotyping 12 markers from the completely sequenced centromere of chromosome 2 was used to estimate a 1.8% false positive rate. Centromeric haplotypes in the diverse inbreds show evidence of genetic exchange, but LD does not decay with distance, consistent with gene conversion and inconsistent with crossing over. The rate of gene conversion in maize centromeres is estimated at .00001 events per marker per generation. These results provide a clear impetus to investigate both the rate of gene conversion in chromosome arms and the relative importance of gene conversion versus crossing over to genetic exchange in maize and other eukaroytes. Pat Brown, 2010

Zwonitzer and colleagues report QTL analysis results from a Ki14 x B73 RIL population after treatments with southern corn leaf blight, gray leaf spot, and northern corn leaf blight. Correlation of infection indices among the disease responses and apparent colocalization of QTL led to the hypothesis that some of the functional polymorphisms may pleiotropically affect disease defense for more than one of the pathogens. After a careful examination of the data and an assessment of potentially confounding phenological effects, the authors concluded that there was no strong evidence for multiple disease resistance QTL in this study, although they leave open the possibility that genetic factors that affect these traits pleiotropically may be operating below the threshold for detection. Nick Lauter, 2010

Classical plant morphology states that there is a trade-off between leaf and branch fate, such that when development of one is precocious it is typically at the expense of the other. For example, in many plants including maize, in the inflorescence the leaf component is reduced at the expense of a flowering shoot component such as a flower or in grasses, a spikelet. Through a thorough series of double-labeling RNA in situ hybridization and/or immunohistochemistry experiments, and analysis of a number of double mutants, the authors show that the tsh4 gene controls the allocation of cells between leaf (bract) and meristem (branch) fates in the inflorescences, elucidating a molecular basis for this developmental trade-off within the maize phytomer. Erik Vollbrecht, 2010

This paper shows that Arabidopsis ARGONAUTE 9 (AGO9) controls female gamete formation. Mutations in AGO9 lead to the differentiation of multiple gametic cells that are able to initiate gametogenesis and ovules with two independently developed female gametophytes are found at a high frequency (~40%). Interestingly, mutations in SUPPRESSOR OF GENE SILENCING 3, RNA-DEPENDENT RNA POLYMERASE 6, RNA-DEPENDENT RNA POLYMERASE 2, DICER-LIKE 3 and RNA POLYMERASE IV/V exhibit an identical defect to ago9 mutants. AGO9 preferentially interacts with 24-nucleotide small RNAs (sRNAs) derived from transposable elements (TEs), and its activity is necessary to silence TEs in female gametes and their accessory cells. AGO9-dependent sRNA silencing is crucial to specify cell fate in the Arabidopsis ovule, and that epigenetic reprogramming in companion cells is necessary for sRNA_dependent silencing in plant gametes. Mario A. Arteaga-Vazquez, 2010

Centromere Protein C (CENPC) has a key role in centromere recognition an maintenance by targeting a histone H3 variant known as Centromeric Histone H3 (CENH3). In maize, centromere repeats (40-200 nt in length) are under-methylated and transcribed to produce stable RNAs that is thought to remain bound to chromatin. This study shows that a 122 amino acid region located between exons 9 and 12 in CENPC is the major region that binds DNA, long RNA (from CentC repeats) and 24 nt small RNAs (homologous to CentC repeats) in a non sequence specific fashion. The purified DNA binding region alone is not able to bind DNA efficiently unless single stranded nucleic acids (larger than 10 nt) are present. RNA blot analysis revealed that the native CentC transcripts are predominantly 75 nt (additional discrete bands ~ 40 nt and 24 nt are detected), transcribed from one strand and interestingly, they are not exclusively present at maize centromere cores (although they seem to be more abundant within kinetochore domains). Based on an in vivo expression analysis of wild type CENPC and two mutant variants (YFP fusion proteins), the authors propose a model where CENPC is first recruited to kinetochores by protein-protein interactions and then converted to a functional DNA binding protein by centromeric RNA. Mario A. Arteaga-Vazquez, 2010

Secreted U. maydis effectors have numerous critical roles during various stages of pathogenic development. The Ustilago maydis protein PEP1 is not required for events leading up to membrane-membrane contact and invagination, but yet is required for sustained invasion of this biotroph. Analysis of deletion mutants of Pep1 provides new insights into fungal communication with the host plant. See Annu. Rev. Phytopathol. 2009. 47:423-445 for additional context. Nick Lauter, 2010

This paper provides the most comprehensive analysis to date of the proteome of bundle sheath versus mesophyll cells in the maize leaf. Maize is a highly efficient C4 plant due to the separation of photosynthetic functions into bundle sheath and mesophyll cells. This paper is an advance over other proteomic papers from the same lab due to the identification of many more proteins and the addition of quantitative data, which is a prerequisite for modeling. It is also one of the first proteomic papers to utilize the recently published maize genome assembly, which greatly aided protein identification. Paula McSteen, 2010

The authors reanalyzed data from three QTL studies of grain yield in maize to investigate the genetic basis of heterosis. Each study involved a (Stiff-Stalk x Non-Stiff-Stalk) cross investigated with Design III (each line backcrossed to both parents). Two traits were calculated from the yield data: mean yield across both backcrosses (Z1) and the difference in yield between the two backcrosses (Z2). Interestingly, Z2 had an higher heritability, QTL for Z2 accounted for a higher proportion of the genetic variance, and there was greater congruence of Z2 QTL positions across the three populations. Furthermore, almost all congruent Z2 QTL were found in or near the centromere. These results are consistent with the pseudo-overdominance model of heterosis, in which heterotic haplotypes carry different combinations of closely-linked favorable alleles. Pat Brown, 2010

Horst and colleagues conducted metabolome and transcriptome surveys in an 8 day timecourse following infection with smut compared to mock infection and observed that smut infection sites acts as strong nitrogen sinks. Tracing experiments performed with labeled nitrogen showed that systemic leaves act as the source of nitrogen that supports "tumor" growth. Finally, they showed that increased photosynthetic output and delayed senescence in source leaves resulted from the presence of the strong sink. These experiments demonstrate the potential of this controlled infection system for important further studies on source-sink relations. Nick Lauter, 2010

While not from maize, I think this paper will most likely impact maize research. By combining mutations in three different genes, the authors are able to create a genotype termed MiMe (mitosis instead of meiosis) in which meiosis is totally replaced by mitosis without affecting subsequent sexual processes. When meiosis is replaced by mitosis, ploidy levels are expected to double each generation and this is observed in the progeny of this MiME line (interestingly fertility is dramatically reduced in 8n plants). The three genes afected: At3g57860, Atspo11 and Atrec8 show strong homology to transcripts present in the maize filtered set (www.maizesequence.org). Mario A. Arteaga-Vazquez, 2010

This paper demonstrates proof-of-concept of the ability of engineered "homing" endonucleases to produce targeted disruptions in endogenous genes in maize. This methodology is an alternative to zinc finger nucleases for generating mutations in target genes. The authors identified a site upstream of an endogenous maize gene that matched 8 out of the 22 bp of the target site of the endonuclease which was then engineered by amino acid substitution to cut specifically at the target site. Transformation of maize led to mutations at the target site in 3% of regenerated plants. The endonuclease generates double stranded breaks in DNA which causes small deletions (or insertions) when repaired by non-homologous end-joining. Therefore, this method could be used to cause deletions in virtually any maize gene. Paula McSteen, 2010

The authors compared gene expression between plants carrying a translocation (aneuploid for part of chromosome 6 and triploid for part of chromosome 5) and their wild-type sibs. First, the expression of ~15K maize genes was analyzed by microarray in seedling and meristem-enriched tissues in the two genotypes. 30 genes showing the most significant expression differences between genotypes were then selected for RT-PCR analysis in 6 additional tissues. Many genes without dosage imbalance showed differential expression (trans effects). Both cis and trans effects included clear examples of tissue-specific and qualitative differences in gene expression (ectopic expression, silencing). Pat Brown, 2010 Maize plants lacking or containing extra chromosomal segments (i.e., aneuploids) show syndrome phenotypes that have long been recognized to correlate to the particular aneuploid chromosome regions. The authors analyzed gene expression by microarray in an aneuploid genotype. Exploiting the ease of isolating specific tissues in maize they show that genes within a duplicated segment show predominantly (but not exclusively) quantitative, global changes in gene expression, while a larger number of genes not in the aneuploid segment more frequently show tissue-specific, trans-effect changes. Moreover, trans effects are more commonly qualitative, likely reflecting consequences of disturbed regulatory and/or developmental processes that are propagated to mature tissues. Thus, at the mRNA level an aneuploid syndrome is characterized by a rich combination of dosage (cis-), dosage compensated and trans- effects in both global and tissue-specific patterns. Erik Vollbrecht, 2010

Research articles by Sidorenko et al., and Stonaker et al., in the November 2009 issue of PLoS Genetics demonstrate that mutations in NRPD2/E2a, similar to Arabidopsis NRPD2/E2, the second largest subunit of plant-specific RNA polymerases IV and V, prevent paramutation at multiple loci. In contrast to the single gene in Arabidopsis, maize has three full length genes with overlapping expression patterns, suggesting maize may have a greater diversification of these gene silencing pathways. Lyudmila Sidorenko, 2009

Class 1 KNOX genes like knotted1 have been shown to play a role in maintaining the shoot apical meristem in maize and in many other plants, and to function outside the meristem in various dicot species by contributing to the elaboration of different leaf morphologies. With analysis of the dominant mutant Kn1-DL, the authors provide evidence that kn1 may similarly function in normal leaf development in maize, by establishing proximal-distal patterning and polarity in the leaf primordium. Erik Vollbrecht, 2010

Selection mapping identifies favorable alleles for the trait of interest using genetic materials that have undergone multiple cycles of recombination and selection. An advantage of this approach is that dedicated stocks need not be developed, meaning that experimental work can proceed on materials generated using standard methods for crop improvement. A significant challenge to selection mapping has been distinguishing potential consequences of drift from those of selection. Significantly, Wisser and colleagues offer a novel statistical treatment of this issue, paving the way for further studies using applied-science resources to address basic science questions. Nick Lauter, 2010

Research articles by Sidorenko et al., and Stonaker et al., in the November 2009 issue of PLoS Genetics demonstrate that mutations in NRPD2/E2a, similar to Arabidopsis NRPD2/E2, the second largest subunit of plant-specific RNA polymerases IV and V, prevent paramutation at multiple loci. In contrast to the single gene in Arabidopsis, maize has three full length genes with overlapping expression patterns, suggesting maize may have a greater diversification of these gene silencing pathways. Lyudmila Sidorenko, 2009

This study propose that an interplay between transcriptional enhancing and epigenetic regulation is involved in a very nice example of mosaic gene expression at the p1 locus in maize. Mario Arteaga, 2010

The authors generated 4 RIL populations from crosses between two temperate (B73, B97) and two tropical (CML254, Ki14) inbreds, phenotyped flowering in 4 long-day and 3 short-day environments, and evaluated the photoperiod response. Interestingly, the four major photoperiod response QTL identified in this study (ZmPR1-4) appear to correspond to previously-identified QTL for flowering under long days. Includes a nice discussion of flowering time genes in maize and other cereals. Pat Brown, 2010

All maize geneticists and functional genomics efforts benefit from tools to screen for loss-of-function mutations in genes of interest. Ahern et al 2009 describe the valuable resources they have developed for using the Ds transposon as a mutagen for both forward and reverse genetic screens. As a methods paper, it also includes some useful protocols. Paula McSteen, 2010

Author List: Carol Soderlund, Anne Descour, Dave Kudrna, Matthew Bomhoff, Lomax Boyd, Jennifer Currie, Angelina Angelova, Kristi Collura, Marina Wissotski, Elizabeth Ashley, Darren Morrow, John Fernandes, Virginia Walbot, Yeisoo Yu

To complement the completion of sequencing the maize B73 genome, Soderlund et al. sequenced 27,455 full-length cDNAs from two maize B73 libraries, representing the gene transcripts from most tissues and common abiotic stress conditions.

Author List: Lifang Zhang, Jer-Ming Chia, Sunita Kumari, Joshua C. Stein, Zhijie Liu, Apurva Narechania, Christopher A. Maher, Katherine Guill, Michael D. McMullen, Doreen Ware

Zhang et al. provide a comprehensive analysis of maize miRNA genes and describe results suggesting that mature miRNA genes were highly conserved during their evolution.

By comparing the B73 reference genome to a second inbred line, Springer et al. reveal that maize has surprisingly high levels of structural diversity but also has large genomic regions that have little or no variation.

Author List: Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Daniel Nettleton, Patrick S. Schnable

Fusheng Wei, Joshua C. Stein, Chengzhi Liang, Jianwei Zhang, Robert S. Fulton, Regina S. Baucom, Emanuele De Paoli, Shiguo Zhou, Lixing Yang, Yujun Han, Shiran Pasternak, Apurva Narechania, Lifang Zhang, Cheng-Ting Yeh, Kai Ying, Dawn H. Nagel, Kristi Collura, David Kudrna, Jennifer Currie, Jinke Lin, HyeRan Kim, Angelina Angelova, Gabriel Scara1, Marina Wissotski, Wolfgang Golser, Laura Courtney, Scott Kruchowski, Tina A. Graves, Susan M. Rock, Stephanie Adams, Lucinda A. Fulton, Catrina Fronick, William Courtney, Melissa Kramer, Lori Spiegel, Lydia Nascimento, Ananth Kalyanaraman, Cristian Chaparro, Jean-Marc Deragon, Phillip San Miguel, Ning Jiang, Susan R. Wessler, Pamela J. Green, Yeisoo Yu, David C. Schwartz, Blake C. Meyers, Jeffrey L. Bennetzen, Robert A. Martienssen, W. Richard McCombie, Srinivas Aluru, Sandra W. Clifton, Patrick S. Schnable, Doreen Ware, Richard K. Wilson, Rod A. Wing

By extensively analysing ~1% of the maize genome, Wei et al. demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets.

In an approach that can be adopted in other large-genome species, Wei et al. use a comprehensive physical and genetic framework map to develop a minimum tiling path of over 16,000 BAC clones across the maize B73 genome.

Author List: Fusheng Wei, Jianwei Zhang, Shiguo Zhou, Ruifeng He, Mary Schaeffer, Kristi Collura, David Kudrna, Ben P. Faga, Marina Wissotski, Wolfgang Golser, Susan M. Rock, Tina A. Graves, Robert S. Fulton, Ed Coe, Patrick S. Schnable, David C. Schwartz, Doreen Ware, Sandra W. Clifton, Richard K. Wilson, Rod A. Wing

The construction of the maize optical map represents the first physical map of a eukaryotic genome larger than 400 Mb that was created de novo from individual genomic DNA molecules.

Author List: Shiguo Zhou, Fusheng Wei, John Nguyen, Mike Bechner, Konstantinos Potamousis, Steve Goldstein, Louise Pape, Michael R. Mehan, Chris Churas, Shiran Pasternak, Dan K. Forrest, Roger Wise, Doreen Ware, Rod A. Wing, Michael S. Waterman, Miron Livny, David C. Schwartz

Author List: Ruth A. Swanson-Wagner, Rhonda DeCook, Yi Jia, Tim Bancroft, Tieming Ji, Xuefeng Zhao, Dan Nettleton, Patrick S. Schnable

Author List: Michael A. Gore, Jer-Ming Chia, Robert J. Elshire, Qi Sun, Elhan S. Ersoz, Bonnie L. Hurwitz, Jason A. Peiffer, Michael D. McMullen, George. Grills, Jeffrey Ross-Ibarra, Doreen H. Ware, Edward S. Buckler

Author List: Jean-Philippe Vielle-Calzada,* Octavio Martmnez de la Vega,* Gustavo Hernandez-Guzman, Enrique Ibarra-Laclette, Cesar Alvarez-Mejma, Julio C. Vega-Arregumn, Beatriz Jiminez-Moraila, Araceli Fernandez-Cortis, Guillermo Corona-Armenta, Luis Herrera-Estrella,Alfredo Herrera-Estrella

Jayson Talag, Andrea Zuccolo, Chuanzhu Fan, Aswathy Sebastian, Melissa Kramer, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Beth Miller, Claude Ambroise, Stephanie Muller, Will Spooner, Apurva Narechania, Liya Ren, Sharon Wei, Sunita Kumari, Ben Faga, Michael J. Levy, Linda McMahan, Peter Van Buren, Matthew W. Vaughn, Kai Ying, Cheng-Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, W. Brad Barbazuk, Regina S. Baucom, Thomas P. Brutnell, Nicholas C. Carpita, Cristian Chaparro, Jer-Ming Chia, Jean-Marc Deragon, James C. Estill, Yan Fu, Jeffrey A. Jeddeloh, Yujun Han, Hyeran Lee, Pinghua Li, Damon R. Lisch, Sanzhen Liu, Zhijie Liu, Dawn Holligan Nagel, Maureen C. McCann, Phillip SanMiguel, Alan M. Myers, Dan Nettleton, John Nguyen, Bryan W. Penning, Lalit Ponnala, Kevin L. Schneider, David C. Schwartz, Anupma Sharma, Carol Soderlund, Nathan M. Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K. Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L. Bennetzen, R. Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G. Presting, Susan R. Wessler, Srinivas Aluru, Robert A. Martienssen, Sandra W. Clifton, W. Richard McCombie, Rod A. Wing, and Richard K. Wilson

Author List: Patrick S. Schnable, Doreen Ware, Robert S. Fulton, Joshua C. Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A. Graves, Patrick Minx, Amy Denise Reily, Laura Courtney, Scott S. Kruchowski, Chad Tomlinson, Cindy Strong, Kim Delehaunty, Catrina Fronick, Bill Courtney, Susan M. Rock, Eddie Belter, Feiyu Du, Kyung Kim, Rachel M. Abbott, Marc Cotton, Andy Levy, Pamela Marchetto, Kerri Ochoa, Stephanie M. Jackson, Barbara Gillam, Weizu Chen, Le Yan, Jamey Higginbotham, Marco Cardenas, Jason Waligorski, Elizabeth Applebaum, Lindsey Phelps, Jason Falcone, Krishna Kanchi, Thynn Thane, Adam Scimone, Nay Thane, Jessica Henke, Tom Wang, Jessica Ruppert, Neha Shah, Kelsi Rotter, Jennifer Hodges, Elizabeth Ingenthron, Matt Cordes, Sara Kohlberg, Jennifer Sgro, Brandon Delgado, Kelly Mead, Asif Chinwalla, Shawn Leonard, Kevin Crouse, Kristi Collura, Dave Kudrna, Jennifer Currie, Ruifeng He, Angelina Angelova, Shanmugam Rajasekar, Teri Mueller, Rene Lomeli, Gabriel Scara, Ara Ko, Krista Delaney, Marina Wissotski, Georgina Lopez, David Campos, Michele Braidotti, Elizabeth Ashley, Wolfgang Golser, HyeRan Kim, Seunghee Lee, Jinke Lin, Zeljko Dujmic, Woojin Kim,

Author List: Thomas K. Wolfgruber, Anupma Sharma, Kevin L. Schneider, Patrice S. Albert, Dal-Hoe Koo, Jinghua Shi, Zhi Gao, Fangpu Han, Hyeran Lee, Ronghui Xu, Jamie Allison, James A. Birchler, Jiming Jiang, R. Kelly Dawe, Gernot G. Presting

Wolfgruber and colleagues describe a comprehensive and general approach for mapping centromeres and present a detailed characterization of two maize centromeres.

Baucom et al. report results showing that the maize genome provides a great number of different niches for the survival and generation of a wide variety of retroelements that have evolved differentially to occupy and exploit this genomic diversity.

Author List: Regina S. Baucom, James C. Estill, Cristian Chaparro, Naadira Upshaw, Ansuya Jogi, Jean-Marc Deragon, Richard P. Westerman, Phillip J. SanMiguel, Jeffrey L. Bennetzen

Jia and colleagues demonstrate that the loss of a key component of the RNA-dependent DNA methylation silencing pathway affects the expression of not only transposons but also thousands of genes.

Author List: Yi Jia, Damon R. Lisch, Kazuhiro Ohtsu4$, Michael J. Scanlon, Daniel Nettleton, Patrick S. Schnable

Author List: Sanzhen Liu1, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel Nettleton, Patrick S. Schnable

The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions decorated with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.

Doubled haploids are becoming an increasingly important tool in maize genetics and are coming into wider and wider use. While much of the interest is coming from breeders interested in more quickly bringing new traits to market, the potential value of this approach in more basic genetic programs is tremendous. This paper examines several testcrossing strategies and finds they may be relatively straightforward for DH lines. Cliff Weil, 2009

Induced resistance (Systemic acquired resistance -SAR and Induce systemic resistance-ISR) has been well characterized in dicots. Given the importance of maize it is surprising that so little is known about induced resistance in this crop- or indeed in monocots in general. It is not even clear whether it really exists in maize. Still, there is a preponderance of evidence suggesting that some induced resistance responses analogous to those seen in dicots do exist. This paper presents perhaps the best evidence for induced resistance in maize to date. This is a field crying out for some careful investigation. Balint-Kurti, 2009

It appears that we are soon to be enlightened by the cloning of a second maize flowering time QTL. Randy Wisser, 2009

PUBMED 19661422

A good example of using the Nested Association Mapping (NAM) panel to analyze a trait. Interestingly, and unlike Arabidopsis, there prove to be no large effect QTL on flowering time but many, small effect QTL instead. Cliff Weil, 2009

This paper reports the development of fertile oat-maize addition (OMA) lines carrying B73 and Mo17 chromosomes. These lines serve as complement to the previously reported OMA carrying sweet corn hybrid Seneca 60 chromosomes. The new OMA carrying chromosomes of sequenced genotypes will be especially useful for mapping of non-genic sequences. Lyudmila Sidorenko, 2009

Alternative splicing of transcripts is increasingly of interest and this paper examines factors controlling that as well as examples of the impact that alternative splicing can have. Cliff Weil, 2009

A preview of genome-wide maize copy number variations among inbred lines. Randy Wisser, 2009

An extremely thorough investigation of patterns of DNA methylation, histone modification, smRNAs, and mRNA distribution in maize. Peter Balint-Kurti 2009

PMID: 19749152 [PubMed - as supplied by publisher]

Insight is provided into the molecular mechanism of sister chromatid cohesion in maize, which requires MIS12 function and is essential for normal chromosomal segregation during meiosis I. Mike Scanlon, 2009

PubMed 19661427

List of authors: McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Oropeza Rosas M, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES.

The phenomenon of populations derived from different parents showing different levels of recombination at the same locus is well known in plants. In this paper McMullen et al perform an extremely thorough investigation, using the NAM population, a 5000-line maize mapping population, consisting of a collection of 25 200-line families, to show that variable recombination is a general phenomenon in maize. They show that the average 4-6cM locus had a 2.9-fold variation in recombination rate between the highest and lowest families, with several intervals showing 30-fold differences or higher. Two other rather interesting things are reported: There was very little evidence for the presence of QTL effecting genome-wide recombination rates, nor was there any evidence that there had been any non-random assortment of unlinked regions of the genome during the production of the mapping lines. This implies that there were no strong epistatic interactions which affected the general fitness of the derived lines. This paper makes it clear that it is important to choose the right parents for any particular fine mapping project so that recombination in the region of interest is maximized. It also provides a resource for identifying such parents. Peter Balint-Kurti, 2009

Epigenetic components of centromeric speciation can be directed by genetic,structural, or topological, DNA properties. Lyudmila Sidorenko, 2009

This comprehensive study deduces maize's journey through the Americas. Randy Wisser, 2009

Maize has long been an excellent system for employing genetic screens. The Candela and Hake (Nat.Rev.Gen.9:883-892) review gives an excellent overview of the system while the Yi et al paper reports a methodological refinement which facilitates the journey from interesting mutant to interesting gene. Peter Balint-Kurti, 2009

Intricate evolution of the maize genome is exemplified by the structure of a complex allele of the well characterized p1 gene. Lyudmila Sidorenko, 2009

Gene targetting, the site-specific alteration of selected genes, has long been possible in mice and other animal systems. An efficient system for gene targetting in plants has however remained elusive. In these papers (two research papers and a commentary) the first efficient systems for site-specific genome alteration in plants are described. Both use zinc-finger nucleases selected in vitro for activity against specific sequences to cause both deletions and insertions in the selected genes. This would seem to open up the possibility of more precisely-engineered transgenic plants which may go some way to alleviating regulatory and consumer-acceptance problems. Peter Balint-Kurti, 2009

OUTER CELL LAYER4 (OCL4) is a maize HD-ZIP IV gene that exhibits tissue layer-specific expression in L1 of shoot meristems and in the epidermis of lateral organ primordia. Recessive loss of function mutations in OCL4 condition ectopic macrohair development on the L1-derived leaf margins, and extra subepidermal layers in the anther locule that correlate with male sterility. The data reveal a role for OCL4 in suppression of margin trichome development and control of epidermal patterning in developing anthers. Mike Scanlon, 2009

A PNAS Darwinian tributary issue includes a paper on maize, revealing a large selective sweep on chromosome 10. Randy Wisser, 2009

Gene targetting, the site-specific alteration of selected genes, has long been possible in mice and other animal systems. An efficient system for gene targetting in plants has however remained elusive. In these papers (two research papers and a commentary) the first efficient systems for site-specific genome alteration in plants are described. Both use zinc-finger nucleases selected in vitro for activity against specific sequences to cause both deletions and insertions in the selected genes. This would seem to open up the possibility of more precisely-engineered transgenic plants which may go some way to alleviating regulatory and consumer-acceptance problems. Peter Balint-Kurti, 2009

Robertson hypothesized that mutant alleles represent extreme variants at the same genes where subtle or quantitative alleles can be found. Maniacci et al. used association mapping to characterize the effects of natural maize allelic variation at Opaque2—a gene previously characterized through the analysis of an opaque2 mutant allele. The associations detected by Maniacci et al. support Robertson’s hypothesis. The author’s further report significant epistatic associations between Opaque2 and a gene it is known to regulate. This study nicely demonstrates the use of detailed knowledge of the physiological processes and genes affecting a phenotype to examine naturally-occurring variation. Randy Wisser, 2009

A new user-friendly search engine named TARGeT (Tree Analysis of Related Genes and Transposons) provides rapid identification of predicted gene structure and gene family members from a variety of plant genome databases, and constructs phylogenetic trees from nucleic acid or DNA sequence queries. Mike Scanlon, 2009

The ability to precisely mutate/repair/replace a gene in its original genomic location is highly desirable. This report demonstrates that this can now be done in maize. Engineered zinc-finger nucleases are used to induce double stranded breaks in a target genomic site that is subsequently patched by a homology directed repair mechanism from a co-transformed donor plasmid. Lyudmila Sidorenko, 2009

Plant disease resistance (R) genes encode proteins that respond to pathogen ingress by triggering a rapid, localized "hypersensitive reaction" (HR), in which host tissue immediately adjacent to the site of pathogen ingress undergoes programmed cell death. Here the authors demonstrate that R-genes can be subverted by necrotrophic pathogens for their own ends. Using a host-specific toxin, Periconia circinata 'deliberately' triggers HR in Sorghum via the dominant Pc susceptibility gene- a gene that, as shown in this paper, has all the sequence features typically associated with R-genes. A similar situation pertains in the Vb/Victorin Victoria blight system in oats. It seems likely that many other examples of this type of interaction will be identified in the next few years. Peter Balint-Kurti, 2009

The parasitic plant Striga infests over 60% of the cultivated land in sub-Saharan Africa, where it can cause complete yield losses of maize, sorghum, cowpeas, and other staple crops. This paper shows that hairpin RNA silencing constructs engineered into lettuce can silence target genes in the parasitic plant Triphysaria, a relative of Striga - providing initial proof-of-concept for a very promising strategy to engineer Striga-resistant maize. Peter Balint-Kurti, 2009

Association mapping often relies on molecular markers to infer pedigree information and the number of markers required for accurate pedigree inference is generally unknown. Yu et al. demonstrate the use of model fitting criteria to assess whether an adequate number of markers have been used in an association mapping study. In addition to their analysis of simulated data, data from canine and maize are presented. Randy Wisser, 2009.

New data suggests that the cytokinin two-component RESPONSE REGULATOR ABPHYLL1 may regulate phyllotaxy indirectly, via a complex interplay between cytokinin signaling and auxin transport that controls shoot meristem size. Mike Scanlon, 2009

This paper continues work on B paramutation and the region 100 kb away from the gene that impacts its expression, describing some of the physical interactions that occur. Cliff Weil, 2009

This comprehensive two volume set will keep us tied over for decades to come. Kudos to the editors for putting this together and authors for their contributions. Randy Wisser, 2009

Mutations of the rmr6 locus fail to maintain gene silencing associated with paramutation, but also disrupt normal plant development, presumably via similar defects in gene silencing. Erhard et al demonstrate that the rmr6 locus encodes RNA Pol IV, and that ~24nt sRNAs are significantly reduced in rmr6 mutant individuals. Nevertheless, the specific mechanism by which Pol IV influences gene expression and the abundance of these small RNAs remains enigmatic given that alpha-amanitin insensitive transcripts (as would be expected for Pol IV) are undetectable even when comparing rmr6 mutants relative to their wild-type siblings. Jane Dorweiler, 2009

As interesting as Helitrons are, one problem they have presented is observing their actual movement. Here, at long last, they are caught in the act, shamelessly excising in a public place! Cliff Weil, 2009

Quantitative disease resistance (QDR) in plants is a poorly understood though rather important phenomenon. The first three papers here represent, to my knowledge, the first published reports identifying plant QDR genes. All three are from monocots but are quite distinct from each other in their function. It is noteworthy that none of them are nucleotide binding site/leucine-rich-repeat (NBS-LRR) genes that have been commonly associated with major-gene plant disease resistance. It is likely that in the next few years many more genes with many more distinct functions will be shown to underlie plant QDR. The fourth paper listed here (Poland et al.) attempts to synthesize what is presently known about QDR, including predictions of the type of genes that might underlie it. Peter Balint-Kurti, 2009

This paper attempts to synthesize what is presently known about QDR, including predictions of the type of genes that might underlie it. Peter Balint-Kurti, 2009

Quantitative disease resistance (QDR) in plants is a poorly understood though rather important phenomenon. The first three papers here represent, to my knowledge, the first published reports identifying plant QDR genes. All three are from monocots but are quite distinct from each other in their function. It is noteworthy that none of them are nucleotide binding site/leucine-rich-repeat (NBS-LRR) genes that have been commonly associated with major-gene plant disease resistance. It is likely that in the next few years many more genes with many more distinct functions will be shown to underlie plant QDR. The fourth paper listed here (Poland et al.) attempts to synthesize what is presently known about QDR, including predictions of the type of genes that might underlie it. Peter Balint-Kurti, 2009

Quantitative disease resistance (QDR) in plants is a poorly understood though rather important phenomenon. The first three papers here represent, to my knowledge, the first published reports identifying plant QDR genes. All three are from monocots but are quite distinct from each other in their function. It is noteworthy that none of them are nucleotide binding site/leucine-rich-repeat (NBS-LRR) genes that have been commonly associated with major-gene plant disease resistance. It is likely that in the next few years many more genes with many more distinct functions will be shown to underlie plant QDR. The fourth paper listed here (Poland et al.) attempts to synthesize what is presently known about QDR, including predictions of the type of genes that might underlie it. Peter Balint-Kurti, 2009

Ac-induced translocations, inversions, and deletions were first described by McClintock in classic papers from the golden age of maize genetics. In this article, Zhang et al propose a mechanism involving alternative transposition of closely linked Ac elements that gives rise to these major chromosomal rearrangements. Mike Scanlon, 2009

This comprehensive two volume set will keep us tied over for decades to come. Kudos to the editors for putting this together and authors for their contributions. Randy Wisser, 2009

This is a nice review of genomic selection, which represents a shift in perspective and thus application of marker-assisted selection and is being touted to revolutionize crop improvement. Randy Wisser, 2009

The paper describes three Mutator alleles of a Polycomb group chromatin gene, Mez1, which normally shows imprinting (the maternal allele is expressed in endosperm and the paternal allele is not expressed). In two cases, mez-m1 and mez-m4, maternal inheritance of the Mu allele allows the normally silent paternal copy to be expressed. For a third allele, mez-m2 and, again, for mez-m4, paternally inherited alleles are not silenced. The suggestion is therefore both that the Mu elements have disrupted important cis-acting sequences governing imprinting and that the Mez1 protein itself may be involved in imprinting its own expression. Cliff Weil, 2009

PMID 19204280

Characterization of two mutant alleles at the ameiotic1 locus in maize shows that the Am1 gene is required for the switch from somatic cell cycle to meiosis as well as progression through the leptotene - zygotene transition in meiotic prophase. The gene encodes a novel, fast-evolving, plant-specific protein showing that in contrast to the overall conservation of the key meiotic processes, the mechanism of meiosis initiation vary even between closely related taxa, such as monocots and dicots. Mike Scanlon, 2009.

Drought resistance may well be the next big thing in plant biotechnology with both commercial and non-profit organizations dedicating large research budgets to it. Monsanto has recently been publicizing their efforts in this area (full page ads in the New York Times, New Yorker, etc.). In this paper, authored by scientists from Monsanto and their collaborators at Mendel Biotechnology, a gene conferring drought tolerance in maize and Arabidopsis is described. Peter Balint-Kurti, 2009

Asymmetric cell division is critical for proper development of a number ofcell fates, including the production of subsidiary cells within the stomatalcomplex. While clear that signal transduction was necessary for proper cellfate and orientation, the ligands and receptors of those signals have longremained obscure. Cartwright and colleagues demonstrate that the pan1 andpan2 genes play a role in properly polarizing subsidiary mother cells inpreparation for the required asymmetric division. Consistent with thehypothesis that the guard mother cell is the source of a ligand directingthat polarization, the pan1 gene encodes a leucine-rich repeat receptor-likeprotein. Jane Dorweiler, 2009

The author's present a thorough QTL mapping analysis using the intermated B73xMo17 advanced intercross line population, enabling candidate gene identification in loci resolved to ~1Mb. A key feature of this study is their development and demonstration of novel methods for error rate control and confidence interval construction for composite interval mapping. Randy Wisser, 2009

An excellent addition to the ongoing efforts to unravel the mysteries of sex determination in maize. Acosta and colleagues demonstrate the importance of Jasmonic acid in normal development of the male tassel. Tasselseed1 encodes a lipoxygenase required for one of the early steps in the JA biosynthesis pathway. Rescue of both ts1 AND ts2 mutant phenotypes with exogenous JA further supports the original genetic and expression data linking these two loci, and suggests that the predicted dehydrogenase encoded by ts2 may function within the JA biosynthesis pathway as well. Jane Dorweiler, 2009

Positional cloning reveals that the tassel seed1 gene encodes a jasmonic acid biosynthetic enzyme, and illustrates a previously unknown role for jasmonate signaling during selective floral abortion and sex determination in the maize inflorescence. Mike Scanlon, 2009

IN this paper Doehlmann et al investigate the compatible (i.e. susceptible) interaction between Ustilago maydis and maize (maize common smut). In doing so, they undertake one of the first detailed analyses of the maize transcriptional response to pathogenesis. They find persuasive circumtantial evidence that, despite this being a compatible interaction, the fungus is recognized by the host early in the interaction and that the defence response is triggered only for it to be subsequently suppressed. They also find evidence that the development of infected cells is substantially redirected by the pathogen, turning them into sink instead of source cells. Peter Balint-Kurti, 2009

A profiling of transcripts associated with male meiosis that finds, in addition to what genes are turned on or off, that there is little new transcription occurring. Signaling of events within the anthers as they progress may thus be based largely on extant mRNAs. This could also have interesting implications for whether recombination is associated with genes that have been transcribed recently. In addition, the data suggest that there are global controls in the anther on gene expression. The authors propose that the expression of as many as 20-25,000 genes during this process serves as a general test of the genome. Cliff Weil, 2009

First the gene-for-gene hypothesis, and more recently the guard model gave us a framework for understanding plant pathogen interactions. This paper now posits the 'decoy model' which persuasively suggests that the host plant may, in a sense, bait traps for the pathogen to blunder into. This model is an important refinement of our understanding of gene-for-gene systems. Peter Balint-Kurti, 2009.

This short review summarizes the latest advances in our understanding of the interplay between auxin and cytokinin during development of the highly modified grass inflorescence. Mike Scanlon, 2009.

A look at the histone code in maize somatic cells finds the distribution of modifications on maize chromosomes is a little different than in Arabidopsis and different than in animals. In addition, CENH3 proves to be very low on maize B chromosome centromeres, raising an interesting possibility that this may help explain their unusual behavior. Cliff Weil, 2009

Using a battery of population genetic analyses the authors present evidence for selective sweeps and divergent selection across a 350kb maize genomic region and guess who's there: Teosinte branched1 and Dwarf8 along with functional flowering time associations in the region under divergent selection. Randy Wisser, 2009.