Genome-wide Association Studies Of Cold Tolerance Genes At Seedling Stage And Bacterial Blight Resistance Genes In Rice

Rice is a staple food for people worldwide.Yield loss of rice caused by biotic and abiotic agents will endanger food safety.Cold damage and bacterial blight disease caused by Xanthomonas oryzae represent respectively one of the abiotic and biotic factor.Resarch on the genetic basis of rice in response to these factors is the foundation for improving rice.In this study,we performed QTL mapping by using genome-wide association study(GWAS)on tolerance to cold and resistance to bacterial blight in rice.The main results as followed:1.295 rice cultivars in the rice diversity panel 1(RDP1),which were collected from 82 countries,were treated under 8℃ at the seedling stage(CTS)to evaluate the cold tolerance score.The results indicate that both temperate and tropical japonica rice cultivars are more tolerant to cold stress than indica and AUS cultivars when compared within six subpopulation of rice.2.Using the cold tolerance phenotypes and 44 K SNP chip dataset of RDP1,we performed genome-wide association mapping of quantitative trait loci(QTLs)for CTS.The analysis identified 67 QTLs for CTS that are located on 11 chromosomes.Fifty-six of these QTLs are located in regions without known cold tolerance-related QTLs.3.To identify candidate genes that are localized in the CTS QTL regions,we analyzed a500 kb genomic region by comparing the QTL regions with the Nipponbare reference genome.Interestingly,we found that the candidate gene LOC_Os03g09140 on chromosome 3.4.Further allele frequency analysis with the 181 associated SNPs revealed that over70% loci in the 20 tolerant cultivars are tolerant SNP types,suggesting that GWAS is a reliable way to detect cold tolerant QTLs in rice.5.The resistance of 271 rice cultivars in the RDP1 to three Xanthomonas oryzae races were tested.6 cultivars demonstrated high resistance against all three races,and 44 cultivars demonstrated high susceptibility.Highly resistant cultivars can be used as germplasm resource for resistance breeding.6.The resistance phenotype of 271 rice cultivars in the RDP1 in response to PX099,P2,J12.Combining the 700,000 newly published SNP genotyping,291 SNP(-logp ≥ 5)closelyrelated to resistance were located with the employment of GWAS system.All tightly associated SNP was assigned to 118 QTLs,including 55 QTLs for PXO99 resistance which covered 172 closely related SNP,59 QTLs for P2 resistance which covered 114 closely related SNP,12 QTLs for J12 resistance which covered 29 closely related SNP.Those revealed 5 known genetic loci,and resistant genes had been cloned.Those genes were xa5、xa13、Xa21、Xa27 and Xa3/Xa26.7.We further analyzed the closely related SNP allele from 6 highly resistant and 44 highly susceptible cultivars to Xanthomonas oryzae.Results revealed that,among those 291 SNP,84 SNP exhibited over 80% phenotype interpretation rate to 6 highly resistant and 38 highly susceptible cultivars.Especially for the 6 highly resistant cultivars,the interpretation rate was over 90%.Therefore,those 84 SNP can be utilized as the molecular marker-assisted selection of highly resistant cultivars.8.Analysis also revealed that,11 loci carried resistance against two of those three Xanthomonas oyzae races,including 21 QTLs and 49 closely related SNP.1 locus carried resistance against all three races,including 4 QTLs and 7 closely related SNP.With the assistance of rice genome and gene annotation data,we selected the gene candidates among those QTLs which carried resistance against at least two Xanthomonas oyzae races.Taken together,rice cold-resistant and rice bacterial blight resistant QTLs were localized with the employment of GWAS.Those QTLs covered part of already known QTLs,and also included QTLs discovered in this research.Moreover,highly resistant rice cultivars against cold and Xanthomonas oryzar pv.oyzae were identified.The rice germplasm resource for cold-tolerance and bacterial blight resistance was replenished by our research,which would provide available resource for further clone novel cold tolerance and bacterial blight resistance genes in rice.