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Bacterial blight, which is caused by  Xanthomonas oryzae  pv.  oryzae  ( Xoo ), is one of the most devastating rice diseases worldwide. The development and use of disease-resistant cultivars have been the most effective strategy to control bacterial blight. Identifying the genes mediating bacterial blight resistance is a prerequisite for breeding cultivars with broad-spectrum and durable resistance. We herein describe a genome-wide association study involving 172 diverse  Oryza sativa  ssp.  indica  accessions to identify loci influencing the resistance to representative strains of six  Xoo  races. Twelve resistance loci containing 121 significantly associated signals were identified using 317,894 single nucleotide polymorphisms, which explained 13.3–59.9% of the variability in lesion length caused by  Xoo  races P1, P6, and P9a. Two hotspot regions (L11 and L12) were located within or nearby two cloned  R  genes ( xa25  and  Xa26 ) and one fine-mapped  R  gene ( Xa4 ). Our results confirmed the relatively high resolution of genome-wide association studies. Moreover, we detected novel significant associations on chromosomes 2, 3, and 6–10. Haplotype analyses of  xa25 , the  Xa26  paralog ( MRKc ;  LOC _ Os11g47290 ), and a  Xa4  candidate gene ( LOC _ 11g46870 ) revealed differences in bacterial blight resistance among  indica  subgroups. These differences were responsible for the observed variations in lesion lengths resulting from infections by  Xoo  races P1 and P9a. Our findings may be relevant for future studies involving bacterial blight resistance gene cloning, and provide insights into the genetic basis for bacterial blight resistance in  indica  rice, which may be useful for knowledge-based crop improvement.

Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm