Genic and nongenic contributions to natural variation of quantitative traits in maize
- Xianran Li1,
- Chengsong Zhu1,
- Cheng-Ting Yeh2,
- Wei Wu2,
- Elizabeth M. Takacs3,
- Katherine A. Petsch4,
- Feng Tian5,
- Guihua Bai1,6,
- Edward S. Buckler5,6,
- Gary J. Muehlbauer7,
- Marja C.P. Timmermans4,
- Michael J. Scanlon3,
- Patrick S. Schnable2,8 and
- Jianming Yu1,8
- 1Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA;
- 2Center for Plant Genomics and Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA;
- 3Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA;
- 4Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 5Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA;
- 6United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Manhattan, Kansas 66506, USA;
- 7Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
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 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.
Footnotes
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↵8 Corresponding authors
Email jyu{at}ksu.edu
Email schnable{at}iastate.edu
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.140277.112.
Freely available online through the Genome Research Open Access option.
- Received March 7, 2012.
- Accepted June 7, 2012.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
