Genetic Dissection Of The Bacterial Blight Disease Resistance In Super Hybrid Rice RILs Using Genome-wide Association Study

Rice is one of the most important crops in the word,ensuring its product security is crucial at the national and global levels.However,bacterial blight caused by Xanthomonas oryzae pv.oryzae is the most destructive bacterial disease in the rice production.Breeding practice has well demonstrated that cultivating new disease-resistance variety by mining and utilizating the novel disease resistance genes is one of the most effective ways to control this disease.Bacterial blight resistance is a complex quantitative trait,and its genetic variation is affected by gene effect、genetic population structure and environment.Conbining multiple genetic population,the analysis model of genome wide association analysis can analyze the genetic background of the complex traits in rice.In our study,a population of 139 recombinent inbred lines（RILs）derived from super hybrid rice Xieyou9308,between the parents of which there is genetic difference in resistance to bacterial blight,were inoculated with four Xoo strains.A genome-wide association study was carried out using 476,505SNPs for the lesion length as a quantitative phenotype.The main conclusions are as follows:（1）The result revealed that a total of 109 significant SNPs were detected at the significant level of p<1×10^-4 for four Xoo strains-treated lesions,which accounted for 59.78%to 63.29%of phenotype variation,respectively.87 genes were obstained by referring to the Nipponbare reference genome.These significant loci are distributed on the 12 chromosomes of rice and the chromosome 12 and chromosome6 show significant peaks.Furthermore,25 SNPs that are located in/nearby 19 candidate genes including two genes（LOC＿os11g43420 and LOC＿os11g45930）encoding NBS-LRR containing proteins were identified by the CR4 inoculation,which account for 61.00%.（2）Gene function prediction and expression analysis of two selected candidate genes,LOC＿Os11g43420 and LOC＿Os11g45930,demonstrated their higher expression levels in the resistant cultivar Zhonghui9308 than in the susceptible variety Xieqingzao B,with a fold of 4.42 and 8.86,suggesting that these two genes positively regulates bacterial blight resistance.Phylogenetic tree analysis found that these two genes are different from the previous cloned resistant genes in evolution,suggesting they are novel disease resistance genes.These results laid a theoretical groundwork and provided genetic resources for future resistant breeding in rice.（3）Correlation analysis found that rice bacterial blight resistance is correlated with the effective panicle number,seed setting rate,grain number,and thousand-grains weight.Mostly,the lesion length is positively correlated with the empty grain,grain,and effective panicles number significantly,which the correlation coefficients are 0.30（p≤0.01）,0.20（p≤0.01）,and 0.15（p≤0.01）,respectively.Indicating that rice bacterial blight could affect the yield by indirect influence the effective panicle number,grain number,and seed setting rate.Rice yield is positively correlation with the grain number,effective panicle number,seed setting rate,and thousand-grain weight,with correlation coefficients are 0.09（p≤0.001）,0.40（p≤0.01）,0.39（p≤0.01）,and 0.30（p≤0.01）,respectively.