INVESTIGATION 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,* and Brian J. Steffenson* ,1 *Department of Plant Pathology, § Department of Plant and Microbial Biology, and **Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, † Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, and ‡ United States Department of Agriculture-Agricultural Research Service, Raleigh, North Carolina 27695 ORCID ID: 0000-0001-7961-5363 (B.J.S.) 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-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 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 associ- ated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley. Among the many described fungal diseases of cultivated barley (Hordeum vulgare subsp. vulgare L.), stem rust ranks among the most devastating. The disease has been reported in many areas across the world, but is most important in the northern Great Plains of the USA and Canada as well as in northeastern Australia and eastern Africa (Dill-Macky et al. 1991; Mwando et al. 2012; Steffenson 1992). Yield losses of up to 58% have been reported for the crop in addition to marked reductions in malting quality traits (Dill-Macky et al. 1991; Mwando et al. 2012). Barley can be infected by two stem rust pathogens: Puccinia graminis Pers.:Pers. f. sp. tritici Eriks and E. Henn. (Pgt) (the wheat stem rust fungus) and P. graminis Pers.:Pers. f. sp. secalis Eriks and E. Henn. (Pgs) (the rye stem rust fungus). The former is far more important than the latter across most major production areas. Breeding for stem rust re- sistance became a target trait in North American barley programs after the severe epidemics of the 1930s (Steffenson 1992). Since the mid- 1940s, losses to stem rust in barley have been minimal, due largely to the resistance conferred by a single resistance gene, Reaction to Pucci- nia graminis 1(Rpg1), in widely grown cultivars (Steffenson 1992). However, isolates of both Pgt and Pgs with virulence for Rpg1 have been reported in North America (Martens et al. 1989; Roelfs et al. 1993; Copyright © 2017 Sallam et al. doi: https://doi.org/10.1534/g3.117.300222 Manuscript received May 14, 2017; accepted for publication August 24, 2017; published Early Online August 30, 2017. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Supplemental material is available online at www.g3journal.org/lookup/suppl/ doi:10.1534/g3.117.300222/-/DC1. 1 Corresponding author: Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, 495 Borlaug Hall, St. Paul, MN 55108-6030. E-mail: bsteffen@umn.edu Volume 7 | October 2017 | 3491 Downloaded from https://academic.oup.com/g3journal/article/7/10/3491/6027559 by guest on 25 May 2022