Genome-wide Association Study For Stripe Rust In Wheat Landraces In The Middle And Low Yangtze Valleys Wheat Zone Of China

Wheat(Triticum aestivum L.)is the major crop in China and plays an important role in agricultural production.With the continuous advancement of breeding work,the genetic diversity of modern wheat cultivars has reduced,and a large number of excellent genes have been lost,which resulted in narrow genetic base.Therefore,the exploration of new genetic resources has become the focus of our research works.Wheat landraces not only contain a lot of disease-resistant and stress-resistant genes,but also have rich genetic variation and good affinity.They are important genetic resources for wheat breeding.Wheat stripe rust is an airborne fungal disease caused by Puccinia striiformis f.sp.tritic.It's a serious desease,which not only decreases the yield,but also damages the quality.In order to obtain excellent germplasm resources with stable resistance to stripe rust,one hundred eighty eight wheat landraces in the middle and low Yangtze valleys wheat zone were used to identify the resistance to the stripe rust in adult stage in four different environments(two locations across two years),SSR markers and the DArT-seq(Diversity Arrays Technology,Canberra,ACT,Australia)genotyping-by-sequencing(GBS)platform were used to achieve the genetic diversity,population structure and phylogenetic relationships of wheat landraces in the middle and low Yangtze valleys wheat zone.Based on the linkage-disequilibrium,genome-wide association analysis of resistance to stripe rust was carried out,and analyzed the significant association loci of yield-related traits of wheat landraces with the infection of stripe rust.The main research results are as follows:1.There are 188 accessions in the middle and low Yangtze valleys wheat zone in four different environments(Chongzhou in 2015,Mianyang in 2015,Chongzhou in 2016,and Mianyang in 2016)were evaluated in adult stage.We got 50 wheat germplasm with stable resistances;Combined with resistance analysis of stripe rust at seedling stage,the landraces named Hongmangcao(AS661750)conferred the gene with all stage resistance to stripe rust.2.We identified the landraces by 135 polymorphic SSR markers.There are 961 allelic variations,with 2-17 alleles on each locus and average of 7.1.Genetic diversity analysis showed that the genetic diversity and polymorphism information content(PIC)of the SSR loci were higher at the level of the whole genome,which were 0.2732 and 0.2289,respectively,indicating that the landraces in the middle and low Yangtze valleys wheat zone have high genetic diversity;The genome A(0.2857 and 0.2369)has more diversity than genome D(0.2736 and 0.2305)and genome B(0.2601 and 0.2194)in genetic diversity and PIC by comparing the genome A,B and D.The chromosome 1A(0.3496 and 0.2784)has highest diversity and the chromosome 5A(0.2438 and 0.2076)has lowest dibersity in genetic diversity and PIC by comparing the every chromosome.By analyzing the population structure based on SSR marker genotypes,the wheat landraces in the middle and low Yangtze valleys wheat zone were divided into three sub-groups.3.Using the DArT-seq markers to perform genome-wide analysis of wheat landraces in the middle and low Yangtze valleys wheat zone,a total of 7099 effective markers were obtained.The analysis of genetic diversity showed that the genetic diversity and polymorphism information content(PIC)of the DArT loci were 0.3150 and 0.2570 at the whole genome level.The A genome and D genome had the highest(0.3158)and lowest(0.3147)gene polymorphism index respectively,while the B genome and D genome had the highest(0.2573)and the lowest(0.2560)PIC,respectively;Further,the 2A chromosome showed the highest genetic diversity(0.3574 and 0.2847),and the 2D chromosome had the lowest genetic diversity(0.2867 and 0.2356).By analyzing the population structure of the DArT-seq markers,the wheat landraces in the middle and low Yangtze valleys wheat zone were divided into three sub-groups.The first subgroup(GP1)was derived from Jiangsu Province,Zhejiang Province and Hubei Province;the second subgroup(GP2)came from Hubei Province;the third subgroup(GP3)was from Hubei Province and Jiangsu Province.4.The association analysis of resistance to stripe rust of 188 landraces based on SSR markers.A total of 13 associated loci were detected.Among them,five loci were significantly associated with resistance at seedling stage which located on chromosomes 2B,4B,5A,6B,and 7D,respectively;eight loci were significant associated with resistance at adult stage,which located on chromosome 1B,3B,4A,4D,5B and 6B.Combined with the constructed wheat stripe rust resistance gene homogeneity map,it showed that the SSR markers Xwmc94-7D,Xcfd4-3B,Xgdm125-4D,and Xgwm499-5B controlling the wheat stripe rust resistance might be new.Moreover,the locus identified by Xgwm499-A4 was excellent allelic locus for area under disease progress curve(AUDPC),diseases index(DI)and disease severity(DS)for stripe rust,the Xgdm125-A3 was another excellent allelic locus for infection type(IT)of stripe rust based on the null allele method reported by Breseghello.5.A genome-wide association analysis of wheat stripe rust resistance was performed on the wheat landraces in the middle and low Yangtze valleys wheat zone using DArT-seq markers.A total of 18 loci significantly associated with resistance to stripe rust.Of them,fourteen loci were significantly associated with the stripe rust in seedling stage,which located on chromosome 1A,1B,2B,3A,3B,4A,5A,5B,6A and 7D;four were significantly associated with adult stage rust resistance,and were located at 1B,2B and 3B respectively.Combined the DArT 3.0 marker genetic map(Diversity Arrays Technology,http://www.diversityarrays.com/)with the constructed consensus map of wheat stripe rust resistance genes,QITsicau-3A.2,QITsicau-4A.1,QITsicau-5A,QITsicau-5B,and QITsicau-7D might be new loci for resistance to stripe rust.6.The association analyses were performed for yield related traits of 188 wheat landraces with inoculation.A total of 29 SSR markers associated with yield-related traits were detected.Among them,six markers were associated with tillering,three loci associated with effective tillers,two loci associated with spike length,three loci associated with spikelet number,eleven loci associated with kernel number per spikelet,five loci associated with kernel number per spike,four loci associated with kernel weight per spike and two loci associated with thousand-kernel weight.Further analysis revealed that Xpsp3000-1B,Xbarc232-1D,Xcfd2-2D,Xbarc148-1D,Xbarc151-5A,Xcfd49-6D,and Xgwm518-6B were significantly associated with multiple yield-related traits,indicating they were pleiotropic.A total of 29 DArT-seq markers were associated with yield traits: among them,nine loci associated were associated with tillering,eleven loci associated with effective tillering,four loci associated with spikelet number,four loci associated with spike length,and one loci associated with thousand-kernel weight.Further analyses have found that 10 DArT-seq markers were associated with total tillering and effective tillering at the same time.These sites might control both total tillering and effective tillering.Further analyses revealed that 9 SSR loci and 13 DArT loci have genetic implicative effects on stripe rust resistance.