Genome-wide association studies of 14 agronomic traits in rice landraces
Top Cited Papers
- 24 October 2010
- journal article
- Published by Springer Science and Business Media LLC in Nature Genetics
- Vol. 42 (11), 961-967
- https://doi.org/10.1038/ng.695
Abstract
Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.Keywords
This publication has 38 references indexed in Scilit:
- Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred linesNature, 2010
- Mixed linear model approach adapted for genome-wide association studiesNature Genetics, 2010
- Genomewide SNP variation reveals relationships among landraces and modern varieties of riceProceedings of the National Academy of Sciences of the United States of America, 2009
- A second generation human haplotype map of over 3.1 million SNPsNature, 2007
- Fire and flood management of coastal swamp enabled first rice paddy cultivation in east ChinaNature, 2007
- Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controlsNature, 2007
- Principal components analysis corrects for stratification in genome-wide association studiesNature Genetics, 2006
- A unified mixed-model method for association mapping that accounts for multiple levels of relatednessNature Genetics, 2005
- A haplotype map of the human genomeNature, 2005
- The map-based sequence of the rice genomeNature, 2005