Genome Wide Association Study (GWAS) and Identification of Novel Rice Blast Resistance Genes

Blast is a cosmopolitan disease causing yield losses and decreasing grain quality in rice-grown regions, and the very fast evolving fungal pathogen, Magnaporthe oryzae, has evolved a repertoire of effectors to nullify rice defense responses. In this study, we developed an integrated strategy to rapidly clone new resistance (R) genes against M. oryzae by combining the genome-wide association study (GWAS) and transcription activator-like effector nuclease (TALEN)/Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) techniques. A total 295 rice accessions including 137 Heuristic Set accessions (HS) and 158 Korean Bred varieties (KB) were screened for the resistance genes. To quantify the disease symptoms, real-time PCR was employed in combination with the primer pair and Taqman probe specific to M. oryzae HYDROPHOBIN class 1 (MHP1) using the DNA samples from the rice leaves infected with compatible or incompatible strains of M. oryzae. After the complete blast evaluation for the whole population, GWAS were performed to examine the associated genes involved in blast resistance. NH1 and NH2, the hub genes relaying main rice defense signaling, were also chosen to analyze its function through knock out strategy. TALEN and Cas9 vectors were constructed and transferred into the resistant cultivars to validate gene function. Resistance of the transgenic plants is being evaluated in the interaction with the pathogen strains. Our results will elucidate a highly efficient method for dissecting the complex genetic architecture and identifying new R blast resistance genes.