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1. Genotypic and phenotypic characterization of a large, diverse population of maize near‐isogenic lines

   https://doi.org/10.1111/tpj.14787  

   Morales, Laura ; Repka, A. C. ; Swarts, Kelly L. ; Stafstrom, William C. ; He, Yijian ; Sermons, Shannon M. ; Yang, Qin ; Lopez‐Zuniga, Luis O. ; Rucker, Elizabeth ; Thomason, Wade E. ; et al ( May 2020 , The Plant Journal)

   Genome‐wide association (GWA) studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping (NAM) can further assess allelic series. Near‐isogenic lines (NILs) can be used to characterize, dissect and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height and resistance to three foliar diseases, and genotyped with genotyping‐by‐sequencing. Across traits, broad‐sense heritability (0.4–0.8) was relatively high. The 896 genotyped nNILs contain 2638 introgressions, which span the entire genome with substantial overlap within and among allele donors. GWA with the whole panel identified 29 QTL for height and disease resistance with allelic variation across donors. To date, this is the largest and most diverse publicly available panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize NAM population in a B73 background combined with data on six agronomically important traits and from genotyping‐by‐sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions, and could readily be used for future fine mapping studies.

    

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2. Elucidating the patterns of pleiotropy and its biological relevance in maize

   https://doi.org/10.1371/journal.pgen.1010664  

   Khaipho-Burch, Merritt ; Ferebee, Taylor ; Giri, Anju ; Ramstein, Guillaume ; Monier, Brandon ; Yi, Emily ; Romay, M. Cinta ; Buckler, Edward S. ( March 2023 , PLOS Genetics)

   Qu, Li-Jia (Ed.)

   Pleiotropy—when a single gene controls two or more seemingly unrelated traits—has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56–32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low.

    

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3. The genetic architecture of teosinte catalyzed and constrained maize domestication

   https://doi.org/10.1073/pnas.1820997116  

   Yang, Chin Jian ; Samayoa, Luis Fernando ; Bradbury, Peter J. ; Olukolu, Bode A. ; Xue, Wei ; York, Alessandra M. ; Tuholski, Michael R. ; Wang, Weidong ; Daskalska, Lora L. ; Neumeyer, Michael A. ; et al ( March 2019 , Proceedings of the National Academy of Sciences)

   The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance–covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.

    

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4. Use of virus‐induced gene silencing to characterize genes involved in modulating hypersensitive cell death in maize

   https://doi.org/10.1111/mpp.12999  

   Murphree, Colin ; Kim, Saet‐Byul ; Karre, Shailesh ; Samira, Rozalynne ; Balint‐Kurti, Peter ( October 2020 , Molecular Plant Pathology)

   Plant disease resistance proteins (R‐proteins) detect specific pathogen‐derived molecules, triggering a defence response often including a rapid localized cell death at the point of pathogen penetration called the hypersensitive response (HR). The maizeRp1‐D21gene encodes a protein that triggers a spontaneous HR causing spots on leaves in the absence of any pathogen. Previously, we used fine mapping and functional analysis in aNicotiana benthamianatransient expression system to identify and characterize a number of genes associated with variation inRp1‐D21‐induced HR. Here we describe a system for characterizing genes mediating HR, using virus‐induced gene silencing (VIGS) in a maize line carryingRp1‐D21. We assess the roles of 12 candidate genes. Three of these genes,SGT1,RAR1, andHSP90, are required for HR induced by a number of R‐proteins across several plant–pathogen systems. We confirmed that maize HSP90 was required for fullRp1‐D21‐induced HR. However, suppression of SGT1 expression unexpectedly increased the severity ofRp1‐D21‐induced HR while suppression of RAR1 expression had no measurable effect. We confirmed the effects on HR of two genes we had previously validated in theN. benthamianasystem,hydroxycinnamoyltransferaseandcaffeoyl CoA O‐methyltransferase. We further showed the suppression the expression of two previously uncharacterized, candidate genes,IQ calmodulin binding protein(IQM3) andvacuolar protein sorting protein 37, suppressedRp1‐D21‐induced HR. This approach is an efficient way to characterize the roles of genes modulating the hypersensitive defence response and other dominant lesion phenotypes in maize.

    

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5. Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

   https://doi.org/10.1093/plphys/kiab073  

   Liang, Zhikai ; Anderson, Sarah N ; Noshay, Jaclyn M ; Crisp, Peter A ; Enders, Tara A ; Springer, Nathan M ( February 2021 , Plant Physiology)

   null (Ed.)

   Abstract Transposable elements (TEs) pervade most eukaryotic genomes. The repetitive nature of TEs complicates the analysis of their expression. Evaluation of the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress reveals no evidence for genome-wide activation of TEs; however, some specific TE families generate transcripts only in stress conditions. There is substantial variation for which TE families exhibit stress-responsive expression in the different genotypes. In order to understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. The stress-responsive activation of a TE family can often be attributed to a small number of elements in the family that contains regions lacking DNA methylation. Comparisons of the expression of TEs in different genotypes revealed both genetic and epigenetic variation. Many of the specific TEs that are activated in stress in one inbred are not present in the other inbred, explaining the lack of activation. Among the elements that are shared in both genomes but only expressed in one genotype, we found that many exhibit differences in DNA methylation such that the genotype without expression is fully methylated. This study provides insights into the regulation of expression of TEs in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression variation. The highly repetitive nature of many TEs complicates the analysis of their expression. Although most TEs are not expressed, some exhibits expression in certain tissues or conditions. We monitored the expression of both TE families (using unique and multi-mapping reads) and specific elements (using uniquely mapping reads) in leaf tissue of three maize (Zea mays) inbred lines subjected to heat or cold stress. While genome-wide activation of TEs did not occur, some TE families generated transcripts only in stress conditions with variation by genotype. To better understand the factors that drive expression of TEs, we focused on a subset of families in which we could monitor expression of individual elements. In most cases, stress-responsive activation of a TE family was attributed to a small number of elements in the family. The elements that contained small regions lacking DNA methylation regions showed enriched expression while fully methylated elements were rarely expressed in control or stress conditions. The cause of varied expression in the different genotypes was due to both genetic and epigenetic variation. Many specific TEs activated by stress in one inbred were not present in the other inbred. Among the elements shared in both genomes, full methylation inhibited expression in one of the genotypes. This study provides insights into the regulation of TE expression in normal and stress conditions and highlights the role of chromatin variation between elements in a family or between genotypes for contributing to expression. 

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