Genic and non-genic contributions to natural variation of quantitative traits in maize
- Jianming Yu1,6,
- Xianran Li1,
- Chengsong Zhu1,
- Cheng-Ting Yeh2,
- Wei Wu2,
- Elizabeth Takacs3,
- Katherine Petsch4,
- Feng Tian3,
- Guihua Bai1,
- Edward Buckler3,
- Gary Muehlbauer5,
- Marja Timmermans4,
- Michael Scanlon3 and
- Patrick Schnable2
- 1 Kansas State University;
- 2 Iowa State University;
- 3 Cornell University;
- 4 Cold Spring Harbor Laboratory;
- 5 University of Minnesota
- ↵* Corresponding author; email: jyu{at}ksu.edu
Abstract
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 non-genic 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 efficient, cost-effective GWAS in species with complex genomes can focus on genic and promoter regions.
- Received March 7, 2012.
- Accepted June 7, 2012.
- © 2012, Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
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