Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm.

Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by pv. (). Screening resistant germplasm and identifying resistance () genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate accessions inoculated with two Chinese strains (KS6-6 and GV) and one Philippine strain (PXO99). Based on the 55K SNPs Array dataset of the 359 accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six genes were localized in the , , and loci on chromosome 11 in this collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, in , encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.