Molecular Dissection of the Complex Genetic Architecture of Rice Immunity to the Blast Fungus Magnaporthe oryzae using GWAS

Rice blast is the most severe disease of rice that causes 10-30% rice yield loss annually. Although there is an untapped blast resistance (R) gene repertoire in the rice germplasm collection, mapping and cloning of the resistance genes are still time-consuming and challenging. In this study, we developed an integrated strategy that allow us to rapidly map and clone new R genes against Magnaporthe oryzae by combining the genome-wide association study (GWAS) and RNAi gene-silencing techniques. Five diverse blast isolates collected in five countries were used to inoculate a world-wide collection of 413 diversity rice varieties that are genotyped with high-density SNP chips. GWAS revealed that 66 loci (p<7.6×10^-5) are associated with leaf blast disease resistance to the five isolates. Among them, 53 are new loci and the other 13 loci are located in the known R gene regions. Three major R loci with the highest contributions to the resistance phenotypes are located in the R gene clusters on chromosome 1, 4 and 9, respectively. RNAi constructs targeting the candidate genes on chromosome 4 and 9 were transferred to the resistant cultivars to validate gene function. Preliminary inoculations show that the NBS-LRR gene at the Pi5 locus is required for the resistance to three blast isolates. These results demonstrate that GWAS is a highly efficient method for dissecting the complex genetic architecture of blast resistance and cloning of new resistance genes in rice.