Genome-wide Association Studies of 14 Agronomic Traits in Rice Landraces

Nat Genet. 2010 Nov;42(11):961-7. doi: 10.1038/ng.695. Epub 2010 Oct 24.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture
  • Base Sequence
  • China
  • Chromosomes, Plant
  • Crops, Agricultural / genetics
  • Genetic Variation
  • Genome, Plant
  • Genome-Wide Association Study*
  • Geography
  • Linkage Disequilibrium
  • Oryza / genetics*
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci