A research team led by Prof. HAN Bin, at National Center for Gene Research and Beijing Institute of Genomics, CAS, published an article in Nature Genetics, reporting the construction of a comprehensive haplotype map for rice that they used for genome-wide association studies (GWAS) of 14 agronomic traits.

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. HAN and colleagues 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. They performed 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.

The article entitled “Genome-wide association studies of 14 agronomic traits in rice landraces” was published in Nature Genetics in November 2010. The full text is available online at http://www.nature.com/ng/journal/v42/n11/abs/ng.695.html.

(Figure 4 from article: Genome-wide association studies of grain width and heading date)