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

<div><p>Bacterial blight, which is caused by <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>), 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 <i>Oryza sativa</i> ssp. <i>indica</i> accessions to identify loci influencing the resistance to representative strains of six <i>Xoo</i> 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 <i>Xoo</i> races P1, P6, and P9a. Two hotspot regions (L11 and L12) were located within or nearby two cloned <i>R</i> genes (<i>xa25</i> and <i>Xa26</i>) and one fine-mapped <i>R</i> gene (<i>Xa4</i>). 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 <i>xa25</i>, the <i>Xa26</i> paralog (<i>MRKc</i>; <i>LOC</i>_<i>Os11g47290</i>), and a <i>Xa4</i> candidate gene (<i>LOC</i>_<i>11g46870</i>) revealed differences in bacterial blight resistance among <i>indica</i> subgroups. These differences were responsible for the observed variations in lesion lengths resulting from infections by <i>Xoo</i> 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 <i>indica</i> rice, which may be useful for knowledge-based crop improvement.</p></div>