Li, X. R., Zhu, C. S., Yeh, C. T., Wu, W., Takacs, E. M., Petsch, K. A., Tian, F., Bai, G. H., Buckler, E. S., Muehlbauer, G. J., Timmermans, M. C. P., Scanlon, M. J., Schnable, P. S., Yu, J. M. (December 2012) Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Research, 22 (12). pp. 2436-2444. ISSN 1088-9051
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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.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | GENOME-WIDE ASSOCIATION MAPPING POPULATION GENETIC-VARIATION FLOWERING-TIME WHOLE-GENOME INBRED LINES TRANSCRIPTOME MODEL LEAF ARCHITECTURE |
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing organism description > plant > maize bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism |
| CSHL Authors: | |
| Communities: | CSHL labs > Timmermans lab |
| Depositing User: | Matt Covey |
| Date: | December 2012 |
| Date Deposited: | 19 Dec 2013 15:20 |
| Last Modified: | 19 Dec 2013 15:20 |
| PMCID: | PMC3514673 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/29113 |
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