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

PLoS Genet. 2014 Dec 4;10(12):e1004845. doi: 10.1371/journal.pgen.1004845. eCollection 2014 Dec.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromosome Mapping
  • DNA Copy Number Variations
  • Gene Frequency
  • Genetic Variation*
  • Genome, Plant
  • Genome-Wide Association Study
  • Genotype
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Quantitative Trait, Heritable*
  • Zea mays / genetics*

Grant support

This study was supported by National Science Foundation (www.nsf.gov) grants DBI-0820619 (JGW), DBI–0501700 (NZ), and IOS-1238014 (JGW), the United States Department of Agriculture - Agricultural Research Service (www.ars.usda.gov) (PJB, ESB), and the Max Planck Society (www.mpg.de) (YG, MS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.