Genetic Analysis And Molecular Mapping Of Stripe Rust Resistant Genes In Three Wheat Varieties And Fine Mapping For Adult-plant Resistance Gene YrXZ9104 To Stripe Rust In Wheat

Common wheat(Triticum aestivum L.)is one of most important cereal crops in the world.Stripe rust,or yellow rust,caused by Puccinia striiformis Westend.f.sp.tritici Erikss.(Pst),occurs on wheat(Triticum aestivum L.)worldwide,and causes significant economic losses by increasing the cost of disease-management and reduced grain yield.As one of the most destructive diseases,it occurs periodically in almost all winter wheat-growing regions in China.Chemicals can control stripe rust;however,the application of chemicals can substantially increase the cost of wheat production and may pollute the environment.Planting resistant wheat varieties is considered as a top priority to control this disease.The main results of this study are listed as follows:1.To unravel the genetic architecture of stripe rust resistance,seedlings of 161recombinant inbred lines(RILs)from the cross Avocet S×SN33 were evaluated with two isolates(PST-Lab.1 and PST-Lab.2)of the stripe rust pathogen(Puccinia striiformis f.sp.tritici)in the greenhouse,and the RILs were evaluated in naturally and/or artificially inoculated field sites during two cropping seasons.The RILs and parents were genotyped with the wheat 55K single nucleotide polymorphism(SNP)array.Three genomic regions conferring seedling resistance were mapped on chromosomes 1DS,2AS,and 3DS,and four consistent quantitative trait loci(QTL)for adult-plant resistance(APR)were detected on1BL,2AS,3DL,and 6BS.The 2AS locus conferring all-stage resistance was identified as the resistant gene Yr17 located on 2NS translocation.The QTL identified on 1BL and 6BS likely correspond to Yr29 and Yr78,respectively.An APR QTL on 3DL explaining 5.8–12.2%of the phenotypic variation,is likely to be new.Molecular marker detection assays with the2NS segment(Yr17),Yr29,Yr78,and QYrsn.nwafu-3DL on a panel of 420 current Chinese wheat cultivars and breeding lines indicated that these genes were present in 11.4%,7.6%,14.8%,and 7.4%entries,respectively.The interactions among these genes/QTL were additive suggesting their potential value in enhancing stripe rust resistance breeding materials as observed in the resistant parent.In addition,we also identified two leaf necrosis genes,Ne1 and Ne2,however,the F₁ plants from cross Avocet S×SN33 survived indicating that SN33 probably has another allele of Ne1 which allows to harvest seeds.4.Wheat cultivar Xinong 3517(XN3517)has remained highly resistant to stripe rust in the field for more than ten years.2.In this study,based on Geno Baits Wheat 16K Panel,four consistent QTL with APR,explained major or minor effect across five environments,were mapped on 1BL,2AL,2BL,and 6BS.All the QTL were probably same with previous report gene/QTL,and further study needs to be confirmed it.Finally,the identified Pst resistance loci with their linked polymorphic SNPs,which were used to developed high-throughput markers,should be helpful for marker-assisted selection in wheat breeding programs.3.To identify genes for use in breeding,a biparental population of 186 recombinant inbred lines(RILs)from a cross of the Chinese landrace Mingxian 169 and CIMMYT-derived line P9936 was evaluated in field nurseries either artificially or naturally inoculated in two crop seasons.Each of the RILs and parents was genotyped with the Wheat55K single nucleotide polymorphism(SNP)‘Breeders'array and a genetic linkage map with 8,225polymorphic SNP markers spanning 3,593.37 c M was constructed.Two major quantitative trait loci(QTL)and two minor QTL were identified.The major QTL QYrblu.nwafu-3BS.2and QYrblu.nwafu-7BL on chromosomes arms 3BS and 7BL were detected in all field locations and explained an average 20.4%and 38.9%of phenotypic variation stripe rust severity,respectively.QYrblu.nwafu-3BS.2 likely corresponds to the locus Yr30/Sr2 and QYrblu.nwafu-7BL may be a resistance allele identified previously in CIMMYT germplasm.The other minor QTL had limited individual effects,but increased resistance when in combinations with other QTL.Markers linked to QYrblu.nwafu-7BL were converted to kompetitive allele-specific PCR(KASP)markers and validated in a panel of wheat accessions.Wheat accessions carrying the same haplotype as P9936 at the identified SNP loci had lower average stripe rust severity than the average severity of all other haplotypes.4.In the previous results,the major QTL QYrxz.nwafu-2BL(Yr XZ9104)on chromosome 2BL,conferring APR,was consistently detected across multiple environments.Yr XZ9104,explained a mean phenotypic variation of 28.9%,was mapped from 672.3 to716.6 Mb in the physical map.In order to fine mapping this gene/QTL,six RILs(RIL-32,43,44,53,59,66)derived from Avocet S/Xingzi 9104 population,were used to developed a 5800 F₂ population.Three KASP markers(XZ2B.k3,XZ2B.k7 and XZ2B.k8)with a 12c M interval,were designed to genotype the F₂population,and 535 recombined lines were obtained.When the 535 recombined lines were generated to F₅ through self-crossing,we began to evaluate the phenotype and extract DNA from the wheat leaves.Based on 90K and660K integrated map,seven new KASP markers were designed to detect heterozygous lines in the target physical interval.The genotyping result showed 25 heterozygous lines were obtained,whereas only two of them were well segregated in the phenotypic evaluation.The heterozygous lines were individually harvested,and all seeds planted as a new F₂ population in our stripe rust disease nursery in 2020.In addition,twenty-four susceptible mutants were obtained to confirm the candidate gene.The objective of this study contributed to the fine mapping and cloning of Yr XZ9104,and provided material support and theoretical guidance for the genetic breeding research on stripe rust resistance in wheat.In summary,haplotype analysis showed that Yr17,Yr29 and Yr78 were widely used in Shaanxi wheat cultivars and breedling lines.In addition,fine mapping of the major adult-plant stripe rust resistance gene Yr XZ9104,which laid a foundation for the cloning of this gene and explaination of the resistance mechanism at the adult stage.