Stem rust (caused by Puccinia graminis f. sp. tritici) is a major disease of wheat. To understand the
genetic basis of stem rust resistance in Nebraska winter wheat, a set of 330 genotypes representing two
nurseries (DUP2015 and TRP2015) were evaluated for resistance to a Nebraska stem rust race (QFCSC)
in two replications. The TRP2015 nursery was also evaluated for its resistance to an additional 13 stem
rust races. The analysis of variance revealed significant variation among genotypes in both populations
for stem rust resistance. Nine stem rust genes, Sr6, Sr31, Sr1RSAmigo, Sr24, Sr36, SrTmp, Sr7b, Sr9b,
and Sr38, were expected and genotyped using gene-specific markers. The results of genetic analysis
confirmed the presence of seven stem rust resistance genes. One genotype (NE15680) contained target
alleles for five stem rust resistance genes and had a high level of stem rust resistance against different
races. Single marker analysis indicated that Sr24 and Sr38 were highly significantly associated with
stem rust resistance in the DUP2015 and TRP2015 nurseries, respectively. Linkage disequilibrium
analysis identified the presence of 17 SNPs in high linkage with the Sr38-specific marker. These SNPs
potentially tagging the Sr38 gene could be used in marker-assisted selection after validating them in
additional genetic backgrounds.