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PMID: 22701078 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Genome research ·Vol. 22 ·No. 12 ·2012-12-00 ·Pages 2436-44

Li X, Zhu C, Yeh CT, Wu W, Takacs EM, Petsch KA, Tian F, Bai G, Buckler ES, Muehlbauer GJ, Timmermans MC, Scanlon MJ, Schnable PS, Yu J

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.

MeSH Terms
Chromosome Mapping Genes, Plant Genetic Variation Linkage Disequilibrium Mutation Phenotype Polymorphism, Single Nucleotide Quantitative Trait Loci RNA, Plant/genetics Sequence Analysis, RNA Transcription Initiation Site Transcriptome Zea mays/genetics
Chemicals
RNA, Plant
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Li Xianran
Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA.
Zhu Chengsong
Yeh Cheng-Ting
Wu Wei
Takacs Elizabeth M
Petsch Katherine A
Tian Feng
Bai Guihua
Buckler Edward S
Muehlbauer Gary J
Timmermans Marja C P
Scanlon Michael J
Schnable Patrick S
Yu Jianming
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.140277.112
Published
2012-12-00
Epub
2012-00-14
Pages
2436-44
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC3514673
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.140277.112 PMC Full Text View journal details
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