Genome-wide association mapping of stem rust resistance in hordeum vulgare subsp. spontaneum

Authors: SALLAM, AHMAD - University Of Minnesota; TYAGI, PRIYANKA - North Carolina State University; Brown-Guedira, Gina; MUEHLBAUER, GARY - University Of Minnesota; HULSE, ALEX - University Of Minnesota; STEFFENSON, BRIAN - University Of Minnesota

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2017
Publication Date: 10/5/2017
Citation: Sallam, A., Tyagi, P., Brown Guedira, G.L., Muehlbauer, G., Hulse, A., Steffenson, B.J. 2017. Genome-wide association mapping of stem rust resistance in hordeum vulgare subsp. spontaneum. G3, Genes/Genomes/Genetics. 7:3491-3507.

Interpretive Summary: Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene Rpg1, losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic and foreign pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection consisting of 314 geographically diverse accessions of wild barley for seedling resistance to four races of the wheat stem rust pathogen and one isolate of the rye stem rust pathogen. Based amount of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with race HKHJC to 19.4% with race 92-MN-90. None of the accessions was resistant to all five cultures of stem rust. A genome-wide association study was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-by-sequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to stem rust across all seven barley chromosomes. Three novel loci associated with resistance to races TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to race HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.

Technical Abstract: Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene Rpg1, losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic (QCCJB) and foreign (TTKSK aka isolate Ug99) pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection (WBDC) (314 ecogeographically diverse accessions of Hordeum vulgare subsp. spontaneum) for seedling resistance to four pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) and one isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis, Pgs). Based on a coefficient of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with HKHJC to 19.4% with 92-MN-90. None of the accessions was resistant to all five cultures of P. graminis. A genome-wide association study (GWAS) was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-bysequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to P. graminis across all seven barley chromosomes. Three novel loci associated with resistance to TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.