RT Journal
A1 Li, Xianran
A1 Zhu, Chengsong
A1 Yeh, Cheng-Ting
A1 Wu, Wei
A1 Takacs, Elizabeth M.
A1 Petsch, Katherine A.
A1 Tian, Feng
A1 Bai, Guihua
A1 Buckler, Edward S.
A1 Muehlbauer, Gary J.
A1 Timmermans, Marja C.P.
A1 Scanlon, Michael J.
A1 Schnable, Patrick S.
A1 Yu, Jianming
T1 Genic and nongenic contributions to natural variation of quantitative traits in maize
JF Genome Research 
JO Genome Research 
YR 2012 
FD December 01 
VO 22 
IS 12 
SP 2436 
OP 2444 
DO 10.1101/gr.140277.112 
UL http://genome.cshlp.org/content/22/12/2436.abstract 
AB The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene–targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%–59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions.