Abstract
Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene.HighlightsNovel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.
Highlights
The objectives of this study were to (1) screen a nursery of 270 Nebraska winter wheat genotypes for their resistance to stem rust race (QFCSC), the common race in the United States, (2) identify SNP markers associated with stem rust resistance using Genome-Wide Association Study (GWAS), (3) validate the SNPs associated with the resistance in another Nebraska winter wheat nursery, and (4) determine whether the markers identified in this study are located in genes and examine their potential role in disease resistance using functional annotations
The association set (A-set) was mostly resistant (80% of the genotypes) with L-infection type (IT) ranging from 0 to 5. This result was expected because the previous generations were screened for stem rust resistance and the selection was made using stem rust resistance as one of the selection criteria
The SNPs associated with stem rust in this study can be considered for markerassisted selection (MAS)
Summary
Henn.) is one of the most damaging diseases in wheat (Singh et al, 2006) It occurred frequently in the United States from the 1920s to 1960s and caused up to 50% yield losses (Leonard and Szabo, 2005). In the central United States Great Plains, an area from central Texas through central Nebraska, stem rust was a major disease and caused significant reductions in the wheat grain yield (Eversmeyer and Kramer, 2000). In recent years, stem rust occurs rarely at Nebraska, in part due to the effective selection for stem rust resistance by the USDA-ARS and University of Nebraska–Lincoln (UNL) Wheat Improvement Team for the past 60 years (Baenziger et al, 2001). Identifying genes controlling stem rust resistance by molecular markers is useful to accelerate breeding programs to improve stem rust resistance by identifying the genes, their vulnerabilities, and being able to pyramid multiple genes in wheat (Nisha et al, 2015)
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