A Genome-wide association study of panicle blast resistance (PBR) to Magnaporthe Oryzae in Rice

Abstract Rice blast, caused by Magnaporthe Oryzae (M. oryzae), is one of the most serious diseases all over the world. Development of blast-resistant rice varieties can effectively control the damage of rice blast and reduce the application of chemical pesticides. In this study, 477 sequenced rice germplasms from 48 countries were inoculated and identified at booting stage. We found that 23 germplasms displayed high panicle blast resistance against M. oryzae. 43 quantitative trait loci (QTLs) significantly (P − 4) associated with rice panicle blast resistance were identified by genome-wide association analysis (GWAS). These QTL intervals contain four genes (OsAKT1, OsRACK1A, Bsr-k1 and Pi25/Pid3) have been reported to be involved in rice blast resistance. We select QTLs with -Log10(Pvalue) higher than 6.0 or those detected in two-year replicates, totaling 12 QTLs, for candidate gene analysis. We identified three blast resistance candidate genes (Os06g0316800, Os06g0320000, Pi25/Pid3) based on the significant SNP distribution of annotated gene sequences in these 12 QTL and the difference of expression levels among blast resistant varieties after 72h inoculation. Os06g0316800 encodes a protein similar to Glycine-rich protein, an important component of plant cell walls involved in cellular stress responses and signaling, named as OsGrp6. Os06g0320000 encodes a protein of unknown function DUF953, belonging to the thioredoxin-like family, crucial for maintaining reactive oxygen species (ROS) homeostasis in vivo, named as OsTrxl1. Lastly, Pi25/Pid3 encodes a disease resistance protein, emphasizing its potential significance in plant biology. By analyzing the haplotypes of these 3 genes, we identified the favorable haplotypes with blast resistance, which will provide genetic resources for future rice blast resistance breeding.