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Association mapping across numerous traits reveals patterns of functional variation in maize

hal.structure.identifierCornell University [New York]
dc.contributor.authorWALLACE, Jason
hal.structure.identifierUSDA-ARS : Agricultural Research Service
dc.contributor.authorBRADBURY, Peter
hal.structure.identifierCornell University [New York]
dc.contributor.authorZHANG, Nengyi
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorGIBON, Yves
hal.structure.identifierMax Planck Institute of Molecular Plant Physiology [MPI-MP]
dc.contributor.authorSTITT, Mark
hal.structure.identifierUSDA-ARS : Agricultural Research Service
dc.contributor.authorBUCKLER, Edward S.
dc.date.created2014
dc.date.issued2014
dc.description.abstractEnPhenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ~5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ~800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ~50% more likely to have a paralog than expected by chance, indicating that gene regulation and neofunctionalization are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.
dc.language.isoen
dc.title.enAssociation mapping across numerous traits reveals patterns of functional variation in maize
dc.typeDocument de travail - Pré-publication
dc.typeWorking paper
dc.identifier.doi10.1101/010207
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
hal.identifierhal-02797919
hal.version1
hal.popularnon
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02797919v1
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