Genome-wide Association Study Of Stripe Rust Resistanceand Yield-related Traits Under Stripe Rust Stress In Southern Chinese Wheat Landraces

Wheat stripe rust caused by Puccinia striiformis West.f.sp.Tritici（Pst）is one of the most important wheat diseases around the world,which seriously affects the yield and quality of wheat.Exploring and trans-breeding stripe rust resistance genes for wheat breeding are the most effective,economical and ecological ways to control damage arising from the wheat stripe rust.At present,with the emergence and prevalence of the new physiological race Chinese yellow rust 34（CYR 34）with strong toxicity in various wheat zones in China,most of the resistant genes,including Yr10 and Yr24/Yr26 which are widely used in production of wheat,are gradually weakening or losing.That has aggravated the trend that damage caused by the wheat stripe rust becomes a disaster in Sichuan,Gansu,Qinghai and other western provinces,and made the wheat in China be under the threat of the stripe rust pandemic again.Therefore,it is urgent to accelerate exploration of new resistance genes and breeding of new rensistance varieties at the current stage.In this study,143 landraces from southern wheat region in China are used as research materials.Through the identification of the resistance phenotype of stripe rust single race at the seedling stage and the mixed races in multiple environments at the adult-plant stage,a batch of superior landraces that can be directly applied to the resistance breeding targeting the wheat stripe rust are screened out.In further,the SSR molecular marker and DAr T-seq chip technologies are employed to carry out the genome-wide molecular scanning for landraces from the sothern wheat zones in China,and in combination with the phenotypic-marker genome-wide association analysis（GWAS）,explore the resistance locus or segment to control the stripe rust.Meanwhile,the locus that controls the yield under the wheat stripe rust stress environment is subject to molecular analysis,expecting to provide the molecular basis for wheat disease resistance and yield breeding.The main results are as follows:1.Research materials are subject to the resistance identification at the seedling stage by means of two stripe rust physiological races,CYR32 and CYR34,which have strong toxicity and high prevalence in wheat production in China currently.The results showed a total of 6accessions are resistant to CYR32 at the seedling stage（IT:0-2）,9 accessions are resistant to CYR34 at the seedling stage and 7 accessions are resistant to both of them at this stage.Then,further use mixed strains（CYR32,CYR33,CYR34,G22-14,Su11-4,Su11-5 and Su11-7）composed of stripe rust physiological races or pathogenic types to conduct the stripe rust resistance phenotype identification of landraces at the adult-plant stage in multi-environment.A total of 50 accessions that have stable resistance to the mixed stripe rust physiological races at the adult-plant stage are screened out.In combination with resistant landraces at the seedling,it is found that 3 accessions（Lushan Wheat,Guangtou Wheat and Yuqiu Wheat）are resistant to the wheat stripe rust（CYR32 and CYR34）at all stage.2.Tiller number（TN）,effective tiller（ET）,spike length（SL）,spikelet number（SN）,kernels number of spikelets（KNS）,kernels per spike（KPS）,grain weight per spike（GWS）and thousand kernel weight（TKW）of research materials are subject to phenotypic analysis based on multiple stripe rust stress environments.The results showed traits related to the yield of landraces from southern wheat zones in China have rich phenotypic variations.The variation range of TKW is 9.96-49.04g and Baihua wheat from Ya’an,Sichuan has the largest TKW（41.50g in average）.The variation range of SL is 5.58-18.34cm and the Bendizi wheat from Mile,Yunnan has the longest SL（14.33cm in average）.The variation range of ET is3-18 and Fengxiang Wheat from Tianshui,Gansu has maximum ET（14 in average）.Based on the yield-related trait analysis,16 superior accessions with higher TKW,larger SL,and larger ET in the stress environment are screened out for the wheat breeding.3.Using a linkage map of stripe-rust resistance in wheat,research materials are subject to the genome-wide molecular scanning by means of 8,279 effective molecular markers（including SSR marker and DAr T-seq）.Molecular genetic diversity analysis showed that landraces from southern wheat zones in China have higher genetic diversity,and their genetic diversity value is 0.3309.The genetic diversity analysis of each subgenome shows that subgenome B has the highest genetic diversity（0.3362）,followed by subgenome A,and subgenome D has the lowest genetic diversity（0.3233）.Comparing the genetic diversity of homologous groups,it is found that,Part 6 homologous group has the highest genetic diversity（0.3423）,and Part 5 homologous group has the lowest genetic diversity（0.3194）.Genetic diversity analysis based on chromosome level shows that 6A has the highest genetic diversity（0.3558）and 1D has the lowest genetic diversity（0.3091）.Research materials are subject to the analysis of the Polymorphism Information Content（PIC）.The results show that no matter it is on the whole genome,subgenome,homologous group or chromosome level,the PIC’s trend is consistent with the analysis result of the genetic diversity.The structure analysis of genetic groups has divided the research materials into the Southwest Germplasm Group and Southern China Germplasm Group.4.Base on 8,279 markers,the GWAS was conducted in 143 accessions to identify loci associated with infection type（IT）to stripe rust at the seedling stage,and a total of 19associated markers(-log₁₀（P）?≥?3.0)involved in 17 QTLs were identified,which located on the chromosome 1A,1B,2A,2B,3B,4A,5B,6A,6B,7B and 7D.The range of phenotypic variation explained（PVE）was 8.71%-17.94%.Among them,QYr ITs.sicau-6A.1 located on Chromosome 6A has the highest PVE（17.94%）;while QYr ITs.sicau-7D located on Chromosome 7D has lowest PVE（8.71%）.2 QTLs（QYr ITs.sicau-3B.2 and QYr ITs.sicau-6A.2）were potentially novel through comparing with the reported linkage map of stripe-rust resistance in wheat.5.A GWAS was conducted in 143 landraces to identify loci associated with IT,the final disease severity（FDS）and the area under the disease progress curve（AUDPC）to stripe rust at the adult-plant stage,and a total of 363 associated markers were identified.We selected 15associated markers involved in 15 QTLs that can be identified at least in 2 environments,which located on the chromosome 1A,1B,2A,2B,3B,4A,5B,6A,6B,7B and 7D.The range of PVE was 8.23%-23.77%.Among them,QYr.sicau-5B.1 located on Chromosome 5A has the highest PVE（23.77%）;while QYr.sicau-1B.4 located on Chromosome 7D has lowest PVE（8.23%）.QYra.sicau-6A.1 was potentially novel through comparing with the reported linkage map of stripe-rust resistance in wheat.6.The 8,279 markers were also used in GWAS which conducted in 143 landraces to identify loci associated with yield-related traits（TN,ET,SN,SL,KNS,KPS,GWS and TKW）under the stripe rust stress environment,and a total of 118 associated markers were identified.We selected 12 associated markers involved in 20 QTLs that can be identified at least in 2environments,which located on the chromosome 1B,2A,2B,3A,4B,5B,6A,6B,6D and 7B.The range of PVE was 8.47%-15.98%.Among them,QKNS.sicau-3A.1 located on Chromosome 3A has the highest PVE（15.98%）;while QSN.sicau-6B.1 located on Chromosome 6B has lowest PVE（8.47%）.