QTL Identification Of Rice Blast Resistance At Seedling Stage In Germplasms By Genome-wide Association Analysis

Rice is one of the most important crops worldwide,though rice blast is the most threaten diseases among its three most serious diseases decreasing rice production.To breed and extend blast resistant varieties by molecular breeding strategies would be an economic and effective way to manage rice blast.In the present study,two sets of diverse rice germplasms' resistance to 5 and 3 strong pathogenic blast strains were evaluated,respectively,and the blast resistant varieties were identified.Further more,genetic bases of rice sidling blast resistance combined with genome-wide high density gene-based association and haplotype analysis were dissected;several main-QTL and candidate genes that affecting blast resistance were located;some favorable alleles associated with resistance against blast strains were discovered,which are all providing valuable resistant germplasms and gene resources for improving rice blast resistance by marker-assisted selection(MAS)rice breeding.The main results are summarized as follows:(1)Against 5 strong pathogenic blast strains,a set of worldwide core germplasms' resistance containing 447 xian and geng varieties were evaluated at the seedling stage(Test 1).The results showed large variation of blast resistance in both xian and geng germplasms.Among them,xian varieties were more resistant against HLJ13-856 while more susceptible against GD00-193 than geng varieties,and 8 xian and 12 geng varieties were resistant against all 5 strains.In both germplasms,resistance against GD00-193,GD17-CQ16 and HB1708 were significantly positive correlated among each other.(2)In Test 1,a total of 68 main-effect QTL were identified against 5 blast strains by genome-wide association analysis.Among them,12 QTL affected resistance against 2 or more strains,and 2 QTL were identified in both xian and geng subpopulations.A total of 30 favorable alleles were mined within these 14 loci,which are valuable for improving rice blast resistance by molecular breeding.(3)A total of 2274 accessions in 3000 Rice Genomes Project were evaluated their resistance against 3 strong pathogenic blast strains at the seedling stage(Test 2).The results showed tremendous variations of blast resistance in the group,and the geng subpopulation were significantly more resistant against all three strains than the xian subpopulation.Total of 63 varieties were resistant against all three strains.Resistance against all three strains were significantly positive correlated among each other in all three subpopulations including the mix,xian and geng subpopulation.(4)In Test 2,a total of 86 main-effect QTL were identified against 3 blast strains by genome-wide association mapping strategy.Of them,15 QTL were identified in the two subpopulations(xian and geng)and 3 identified in all three subpopulations(xian,geng and mix).In addition,9 genomic regions were detected affecting resistance against 2 or 3 strains.Using gene-based association mapping and haplotype analysis,15 candidate genes and 21 favorable alleles at 7 important QTL were mined.Distribution of resistant haplotypes at the 15 candidate genes was inferred in the 63 varieties with resistance to 3 strains.The results provided solid basement for further study on analysing molecular mechanism in rice blast resistance,improving rice blast resistance breeding and expanding resistance spectrum by molecular-characteristics-assisted polymerizing different resistant genes.