Sequencing-Based GWAS For Cloning QTLs In Wild and Cultivated Rice

Cultivated rice evolved from its wild progenitor under natural and human selection. Identifying the genetic basis of the diverse varieties will provide important insights for breeding elite varieties for sustainable agriculture. We sequenced 950 world-wide rice varieties including Oryza sativa indica and japonica subspecies, and constructed a high-density haplotype map of rice genome by using a data imputation method. We performed genome-wide association studies (GWAS) for cloning QTLs underlie multiple agronomic traits. The peak signals at six loci tied closely to the previously identified genes. To characterize various gene alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. Candidate genes were identified for some associated loci through detailed annotation, expression profiling and identification of putative causal mutations. Moreover, we sequenced and analyzed the genomes of 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice. Compared with cultivated rice, its wild progenitor O. rufipogon has a higher genetic diversity, a weaker population differentiation and a more rapid LD decay rate, suggesting that the wild rice collection would be an ideal system for GWAS. We phenotyped each accession of the O. rufipogon population for several traits and perform GWAS in the wild population. The details will be presented.