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

Ahmad H. Sallam, Priyanka Tyagi, Gina Brown-Guedira, Gary J. Muehlbauer, Alex Hulse, Brian J. Steffenson

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29 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)3491-3507
Number of pages17
JournalG3: Genes, Genomes, Genetics
Issue number10
StatePublished - Oct 1 2017

Bibliographical note

Funding Information:
We thank Tamas Szinyei, Matthew Martin, and Joy Roy for excellent technical assistance. This research was funded, in part, by the Lieberman-Okinow Endowment at the University of Minnesota, the American Malting Barley Association, the Bill & Melinda Gates Foundation, the UK Department for International Development to Cornell University for the Borlaug Global Rust Initiative Durable Rust Resistance in Wheat Project, and USDA-ARS Cooperative Agreement 58-5062-5-012 (Understanding Stem Rust Resistance in Barley and Germplasm).

Publisher Copyright:
© 2017 Sallam et al.


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