A panel of 283 durum wheat lines from the International Maize and Wheat Improvement Center (CIMMYT) were evaluated at the seedling stage for responses against races TTKSK, JRCQC, TKTTF and TTRTF in the BSL3
facility at the University of Minnesota. The lines were genotyped using genotyping-by-sequencing (GBS) at the USDA-ARS Eastern Regional Small Grains Genotyping Lab in Raleigh, NC. The mean linearized scale of seedling
infection types and 26,439 Single Nucleotide Polymorphism (SNP) markers for 280 lines were used to undertake Genome-Wide Association Analysis (GWAS) and a False discovery rate of 5% was used as a threshold to declare
significant marker-trait associations (MTAs). MLM identified 52, 47, 20 and 71 significant MTAs for responses against races TTKSK, TKTTF, JRCQC and TTRTF, respectively. Among the total MTAs, 1%, 16.6% and 30.7%
were consistent between the four, three and two races, respectively and 51.7% were identified for single race. FarmCPU detected eight, nine, eleven and nine significant MTAs for responses against TTKSK, TKTTF, JRCQC and
TTRTF, respectively. MLM detected a total of 17 QTL while FarmCPU detected 20 QTL and six of them were consistent between the two models. Chromosome 6A harbored the highest number of significant MTAs (70) with the
largest contribution to the phenotypic variation (3.2% to 17.1%). The identified regions matched the location of Sr7a, Sr11, Sr13, Sr17, Sr22, Sr49 and other previously reported loci. Novel loci on chromosomes 2B, 3A, 6A and 7A were consistent between races and the two models and can be used in marker-assisted selection after validation. Two regions on chromosome 6A (611 Mb and 615 Mb) that are postulated as Sr13a and Sr13c based on the race specificity can be used to differentiate the two alleles. The significant markers identified in the current study can be utilized to identify sources of resistance to stem rust. These results, complementing evaluations of field response to Pgt races, would enhance the capacity of durum wheat breeding programs to conduct a more effective effort tackling stem rust resistance breeding.