Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

Nat Genet. 2011 Dec 4;44(1):32-9. doi: 10.1038/ng.1018.


A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Edible Grain / genetics
  • Flowers / genetics
  • Gene Expression Profiling
  • Genes, Plant
  • Genetics, Population
  • Genome-Wide Association Study*
  • Haplotypes
  • Oryza / genetics*
  • Polymorphism, Genetic
  • Sequence Analysis, DNA