title: Association mapping across numerous traits reveals patterns of functional variation in maize.
abstract: Phenotypic 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 gene duplication are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Wallace
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America; United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bradbury
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America.
authors.forename: Nengyi
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Golm-Potsdam, Germany; INRA, UMR 1332, Univ. Bordeaux, Villenave d'Ornon, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Gibon
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Golm-Potsdam, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Stitt
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America; United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America; Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
mesh_terms: D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D005787:Gene Frequency; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D003313:Zea mays / Q000235:genetics*