Dissection of Resistance Loci to Bacterial Leaf Streak in Rice by a Genome-Wide Association Study

Rice (Oryza sativa L.) bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) seriously threatens rice production. This disease can be controlled by cultivating lines with appropriate resistance genes. To discover new resistance loci, a natural population of 246 sequenced backbone varieties of indica rice was inoculated with Xoc in the field, and their disease level was evaluated. The population structure, distribution of resistance phenotypes, and effect of combinations of resistance genes were analyzed in a genome-wide association study. On the basis of single nucleotide polymorphism data and disease phenotypes at the seedling stage, seven resistance loci (qBls1.1, qBls4.1, qBls5.1, qBls7.1, qBls8.1, qBls9.1, and qBls12.1) were identified to determine the superior haplotype of the corresponding loci, which showed stronger BLS resistance. The effects of combining loci were analyzed. As the number of superior haplotypes increased, BLS resistance tended to increase, indicating that BLS resistance can be significantly improved by pyramiding multiple resistance loci in ideal germplasm. This study provides new resistance loci and genetic resources for breeding BLS-resistant rice varieties. These genetic resources will be useful for the fine mapping of resistance loci, gene cloning, and the breeding of BLS-resistant varieties in follow-up research.