Genic and nongenic contributions to natural variation of quantitative traits in maize

• DOI: 10.1101/gr.140277.112
• Publication Date: 2012-06-15T05:29:37Z
• Authors: Xianran Li; Chengsong Zhu; Cheng-Ting Yeh; Wei Wu; Elizabeth M. Takacs; Katherine A. Petsch; Feng Tian; Guihua Bai; Edward S. Buckler; Gary J. Muehlbauer; Marja C.P. Timmer...; Michael J. Scanlon; Patrick S. Schnable; Jianming Yu
• Keywords: Genetic architecture; Genome-wide Association Study; Trait; Genetic Association

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control quantitative traits with great importance in crop production, adaptation, and evolution. Advances genomic technology need be integrated strategic design novel perspectives break new ground. Complementary individual-gene–targeted research, which remains challenging, a global assessment distribution trait-associated SNPs (TASs) discovered from genome scans can provide insights into architecture contribute future studies. Here we report first systematic tabulation relative contribution different regions trait variation maize. We found that TASs were enriched nongenic regions, particularly within 5-kb window upstream genes, highlights polymorphisms regulating gene expression shaping natural variation. Consistent these findings, collectively explained 44%–59% total phenotypic across maize traits, on average, 79% could attributed located genes or 5 kb together comprise only 13% genome. Our findings suggest efficient, cost-effective genome-wide association studies (GWAS) species focus genic promoter regions.