Genetic dissection of the bacterial blight disease resistance in super hybrid rice RILs using genome-wide association study.

Bacterial blight caused by Xanthomonas oryzae pv. oryzae is the most destructive bacterial disease in rice production, and cultivating new disease-resistance variety by mining and utilizing the novel disease resistance genes is one of the most effective ways to control this disease. In our study, a population of 139 recombinant inbred lines (RILs) derived from super hybrid rice Xieyou 9308, between the parents of which there was genetic difference in resistance to bacterial blight, were inoculated with four Xoo strains. A genome-wide association study (GWAS) was carried out using 476,505 SNPs for the lesion length as a quantitative phenotype. The result revealed that a total of 109 significant SNPs including two genes encoding NBS-LRR containing proteins were detected to be significantly difference at P < 1x10^-4 for four Xoo strains-treated lesions, accounting for phenotype variation of 59.78%-63.29%, respectively. Furthermore, 25 SNPs located in/nearby 19 candidate genes were identified by the CR4 inoculation, accounting for 61.00%. Relative expression analysis of two selected candidate genes, LOC_Os11g43420 and LOC_Os11g45930, demonstrated their higher expression levels in the resistant cultivar Zhonghui 9308 than in the susceptible variety Xieqingzao B, suggesting that these two genes might positively regulated bacterial blight resistance. Phylogenetic tree analysis indicated that these two genes were different from the previous cloned resistant genes in evolution, suggesting they were novel disease resistance genes. These results lays a theoretical basis and provides genetic resources for future resistant breeding in rice. [ABSTRACT FROM AUTHOR]