Genome-wide association mapping of loci conferring all-stage and high-temperature adult-plant resistance to stripe rust in a global spring barley collection

Authors: UPADHAYA, ARJUN - Washington State University; WANG, MEINAN - Washington State University; FATIMA, NOSHEEN - Washington State University; BROOKE, MATTHEW - Washington State University; Ruff, Travis; See, Deven; BRUEGGEMAN, ROBERT - Washington State University; Chen, Xianming

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/19/2025
Publication Date: 7/8/2025
Citation: Upadhaya, A., Wang, M., Fatima, N., Brooke, M., Ruff, T., See, D.R., Brueggeman, R., Chen, X. 2025. Genome-wide association mapping of loci conferring all-stage and high-temperature adult-plant resistance to stripe rust in a global spring barley collection. Theoretical and Applied Genetics. 138. Article 176. https://doi.org/10.1007/s00122-025-04963-3.
DOI: https://doi.org/10.1007/s00122-025-04963-3

Interpretive Summary: Stripe rust is an important disease of barley in temperate regions worldwide. Identification and genetic characterization of stripe rust resistance are essential for development and deployment of durable resistance in barley cultivars. A total of 318 spring barley lines from a global barley collection were evaluated for resistance to the stripe rust pathogen at the seedling stageunder the low temperature profile (4-20°C) using five races and at the adult-plant stage under a high temperature profile (15-25°C) using the most predominant race in the greenhouse, and in four field environments in Washington. The frequencies of resistant accessions ranged from 15-54% at the seedling stage and 47-76% at the adult-plant stage. Genome-wide association analysis using 6,332 markers identified 60 significant SNPs corresponding to 44 loci for stripe rust resistance, including 22 for all-stage resistance (ASR) and 22 for high-temperature adult-plant (HTAP) resistance, distributed across all seven barley chromosomes. Three ASR loci and eleven HTAP loci are potentially novel. Five ASR loci and five HTAP resistance loci are major-effect loci, each explaining over 10% of the phenotypic variation. PCR Allele Competitive Extension (PACE) markers were developed for eight broad-spectrum ASR loci, which may facilitate resistance screening and targeted locus introgression in barley breeding programs. The genetic resources developed in this study will be valuable for breeding efforts aimed at enhancing resistance to stripe rust in barley cultivars.

Technical Abstract: Stripe rust is an important disease of barley in temperate regions worldwide. Identification and genetic characterization of stripe rust resistance are essential for development and deployment of durable resistance in barley cultivars. A total of 318 spring barley lines from a global barley collection were evaluated for resistance to the stripe rust pathogen Puccinia striiformis f. sp. hordei (Psh) at the seedling stage in the greenhouse (4-20°C) using five Psh races (PSH-33, PSH-48, PSH-72, PSH-117 and PSH-118) and at the adult-plant stage in the greenhouse under a high temperature profile (15-25°C) and in four field environments in Washington, USA. The frequencies of resistant accessions ranged from 15-54% at the seedling stage and 47-76% at the adult-plant stage. Genome-wide association analysis using 6,332 markers identified 60 significant SNPs corresponding to 44 loci for stripe rust resistance, including 22 all-stage resistance (ASR) loci and 22 high-temperature adult-plant resistance (HTAP) loci, distributed across all seven barley chromosomes. Three ASR loci and eleven HTAP loci are potentially novel. Five ASR loci (QRpsh_1H.3, QRpsh_3H.1, QRpsh_5H.5, QRpsh_5H.6 and QRpsh_7H.4) and five HTAP resistance loci (QRpsh_1H.4, QRpsh_3H.2, QRpsh_4H.3, QRpsh_5H.4 and QRpsh_7H.2) are major-effect loci, each explaining over 10% of the phenotypic variation. PCR Allele Competitive Extension (PACE) markers were developed for eight broad-spectrum ASR loci, which may facilitate resistance screening and targeted locus introgression in barley breeding programs. The genetic resources developed in this study will be valuable for breeding efforts aimed at enhancing resistance to stripe rust in barley cultivars.