Genome-wide Association Study Identify Alleles Controlling Important Agricultural Traits Directly in Rice

Rice (Oryza sativa L.) is the staple food for more than half of the world population. After thousands of years of cultivation, rice landraces have accumulated an enormous of important agronomic traits, which are invaluable genetic resources for breeding elite varieties for sustainable agriculture. Moreover, rice has a high-quality reference genome sequence and the self-fertilization system that allows simplified haplotype identification and repeated phenotyping for GWAS.

Bin Han and his colleagues recently re-sequenced a broad and large sample of world-wide rice cultivars for genotyping extensive sequence variations of rice natural population. They thus performed GWAS to identify the associated loci with complex traits in rice. They also developed a novel analytical framework to assemble low-coverage sequences of different gene alleles. This approach was used to detect single nucleotide polymorphisms (SNPs) and complex polymorphisms such as short insertions and deletions (indels). This facilitated detailed study of any target locus. They demonstrated that the broader sampling greatly enhanced the power of GWAS of complex traits. These results were recently online published in Nature Genetics on December 4th, 2011.

Figure 1 Genetic structure and population differentiation in 950 rice accessions. (a) Neighbor-joining tree of 950 rice accessions constructed from a simple matching distance of 4.1 million SNPs. The five divergent groups, indica (Ind), aus (Aus), temperate japonica (TeJ), tropical japonica (TrJ) and intermediate (Int), are colored in red, purple, blue, cyan and black, respectively. The scale bar indicates the simple matching distance. (b) The distributions of the pairwise population-differentiation statistic (Fst) across the rice genomes between indica and temperate japonica (in black), between temperate japonica and tropical japonica (in blue) and between indica and aus (in red)