Identification and association mapping of sources of stem rust resistance in the wild barley diversity panel effective against virulent isolates from the Pacific Northwest

Identifying and genetically characterizing new sources of resistance in barley (Hordeum vulgare) effective against the virulent wheat stem rust (Puccinia graminis f. sp. tritici [Pgt]) population in the Pacific Northwest (PNW) is critical. Isolates from this population, including Pgt isolate Lsp21, were virulent on barley stem rust resistance (R) genes Rpg1, Rpg2, Rpg3, rpg4, Rpg5, and rpg8. Notably, 10% of the Pgt isolates from the population were virulent on barley line Q21861, which contains Rpg1 and rpg4/5 stacked together. Virulence on these 2 broad and effective stem rust R-genes/loci, when combined, is unprecedented Pgt virulence on barley. To discover novel resistance, 277 wild barley (H. vulgare subsp. spontaneum) accessions from the Wild Barley Diversity Collection (WBDC) were screened with Pgt isolate Lsp21. Twelve percent showed moderate resistance, with WBDC-94 and WBDC-238 from Jordan exhibiting exceptional resistance, likely conferred by Rpg7, previously reported in both. To genetically characterize resistance in the WBDC, a genome-wide association study was conducted using disease reactions to Lsp21 and 37,338 genotyping-by-sequencing SNPs. Twelve resistance-associated loci were identified on chromosomes 1H, 2H, 3H, 5H, 6H, and 7H. Rpg7 was not detected due to its low allele frequency in the panel. Importantly, 7 novel resistance loci, WQRpg-2H01, WQRpg-2H02, WQRpg-3H01, WQRpg-5H01, WQRpg-5H03, WQRpg-7H02, and WQRpg-7H03, were discovered. These new sources of resistance can be integrated into cultivated barley, and the associated SNPs will aid in tracking resistance loci in prebreeding lines, enhancing breeding efforts against the virulent PNW Pgt population.