Genome-wide Association Study For Stripe Rust Resistance At The Adult Plant Stage And Yield-related Traits Under Stripe Rust Stress In Sichuan Wheat

About 165 wheat cultivars were released in Sichuan between 1997 and 2016.By reducing damages from stripe rust especially in Southwest of China,Huang-Huai river and the middle and lower reaches of the Yangtze River,these varieties have made huge contribution to food security in China.Landraces had been widely grown in Sichuan before the founding of the New China.They are characterised by early maturity,and large numbers of flowers and kernels.Importantly,the landraces were widely adapted to the highly varied ecological and geographical environments under high stripe rust pressure.Clearly,understanding the genetic mechanism of stripe rust resistance and yield components,as well as identifying genes underlying these characteristics,would be highly desirable in breeding high-yielding cultivars with stripe rust resistance.In the study reported here,244 wheat accessions originated from Sichuan(including 79 landraces and 165 cultivars)were investigated in multiple environments under stripe rust pressure.Elite accessions with highlevels of stripe rust resistance and high-yielding potential were identified for wheat breeding.A genome-wide association study(GWAS)was conducted against all these accessions with the use of a wheat 55 K SNP(single nucleiotide polymorphism)microarray.This assessment revealed diverse genetic variation among the accessions and it also detected novel QTLs(quantitative trait loci)associated with stripe rust resistance and yield-related traits.Main results obtained from the study include:The wheat 55 K SNP microarray produced 44,059 effective markers which gave an average distance of 0.32 Mb between markers.The range of the major allele frequency,gene diversity and polymorphism information content(PIC)were 0.665-0.778,0.316-0.422 and 0.259-0.329,respectively.These results showed that rich sources of genetic variation exist among the Sichuan wheat accession.Of the three subgenomes of hexaploidy wheat,subgenome B was the most polymorphic.Of the 21 chromosomes in wheat,chromosome 5B was the most polymorphic.The cultivars showed higher levels of genetic diversity for 20 of the 21 chromosomes with chromosome 2A as the exception.The landraces and cultivars were mainly divided into two different sub-populations based on the delta K(?K)method of Bayesian clustering,indicating the existence of significant genetic difference between them.1)Field trials were artificially inoculated with a mixture of virulent races of Puccinia striiformis Westend f.sp.tritic Erikss.(Pst)prevalent in China.Data on reaction to stripe rust was collected at the adult plant stage from multiple environments.Among the 244 accessions assessed,24(including 12 landraces and 12 cultivars)showed highlevels of resistance to stripe rust consistently in all the environments tested.The landraces performed better on average than the cultivars in stripe rust resistance.Yieldrelated traits were evaluated in three environments under stripe rust stress.The range of phenotypic diversity index among the 244 accessions varied from 0.67 to 0.86.Accessions with large spikes(10 accessions),large numbers of fertile tillers(25 accessions)and large thousand-kernel weight(TKW)(10 accessions),were identified.Both kernel number per spike(KPS)and TKW exhibited high diversity indexes,while the fertile tiller number(FTN)and spikelet number per spike(Sl PS)had low diversity indexes.The landraces performed better than the cultivars in FTN,Sl PS,and spikelet compactness(Sl C),and the cultivars performed better than the landraces in KPS,kernel weight per spike(KWPS)and TKW.Compared with FTN,both TKW and Sl C had higher broad-sense heritability(H2).Phenotypic comparison between resistant and susceptible accessions showed that resistance can effectively reduce the losses of KPS,KWPS,and TKW under stripe rust stress.2)A GWAS analysis against the 244 wheat accessions using the 44,059 SNP markers was conducted to identify loci associated with resistance to stripe rust at the adult plant stage.The analysis was based on the mixed linear model(MLM)with Q + K as covariates.A total of 3,744 associated markers(-log10(P)???3.0)were identified.Of them,30 markers associated with 20 different QTLs were detected from at least 3 different environments each.These QTLs were located on the chromosomes 1A,1B,1D,2B,3D,4D,5A,5B,6A,6B,7A,and 7B,respectively.The range of phenotypic variation explained(PVE)by these loci varied from 5.1% to 19.2%.Favorable allelic variations for 28 of these markers were identified.Seven of these QTLs were potentially novel.They had significant genetic effects on reducing stripe rust severity.Furthermore,candidate gene analyses were conducted for each of the seven novel QTLs.These analyses identified 38 candidate genes involved in the signaling pathway of resistance response,the phytohormone for disease resistance,the typical protein/gene structures,and resistance gene families among others.3)The 44,059 SNP markers were also used in GWAS analysis based on MLM(Q + K)to identify loci associated with yield-related traits in three environments under stripe rust stress.A total of 1,995 associated loci(-log10(P)???3.0)were identified.Of them,59markers involved in 35 QTLs which were detected from at least two of the environments.These QTLs were located on the chromosomes 1A,1B,1D,2A,2B,2D,3B,3D,4A,5A,5B,6A,6D,and 7A,respectively.The range of PVE varied from 5.4% to 20.4% and 54 favorable allelic variations were identified from these associated markers.Comparing with those reported previously,we identified 13 potentially novel QTL and they showed significant genetic effects on yield-related traits.We further analyzed the candidate genes of the 13 potentially novel QTLs and identified 50 candidate genes.They were involved in the regulation of phytohormone,cell division and proliferation,meristem development,plant and organ development,carbohydrate synthesis and transport.