Identification of Novel SNPs for Sr6 Stem Rust Resistance Gene in Winter Bread Wheat by using GWAS

Stem rust (caused by Puccinia graminis f. sp.  tritici Erikss. & E. Henn.), is a major disease in wheat. However, in recent years it occurs rarely in Nebraska due to the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, stem rust seedling resistance was evaluated at the seedling stage in two Nebraska winter wheat populations with a total number of 330 genotypes. The evaluation was to eleven stem rust races in one population and Nebraska common race (QFCSC) in the other population. The evaluation was done in two replications for QFCSC race in both populations and in one replication to the remaining races. Based on the pedigree information and the phenotypic infection type of the tested genotypes, Sr6 gene was expected to be found in the tested genotypes. To confirm the presence of this gene in the genome of the tested Nebraska winter wheat genotypes, specific SSR marker was used. In both populations, a high percent of genotypes contained markers for Sr6 gene in their genome. Genome wide association study was done on these populations using 8905 SNPs and 19 SNPs on chromosome 2D were identified to be associated with stem rust seedling resistance (–log10 p values ranged from 6.97 to 8.08). Sr6 gene was mapped on the same chromosome. A high linkage disequilibrium was found between all the 19 SNPs and the specific SSR markers for Sr6 (from 0.5 to 1). These SNPs should be helpful for marker-assisted selection for Sr6 gene.