To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was subjected to paired-end Illumina sequencing at ∼9 × depth and evaluated for several agronomic traits. We discovered 240.2 million single nucleotide polymorphisms (SNPs) after alignment to the Morex V3 assembly and 24.4 million short (1 to 50 bp) insertions and deletions. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1H close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for seedling stem rust resistance, including 2 novel loci on chromosomes 1H and 6H and one co-locating to the complex RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

Agriculture and Agri Food Canada Lacombe Research and Development Centre Lacombe Alberta T4L 1W1 Canada

American Malting Barley Association Inc Brookfield WI 53005 United States

Anheuser Busch InBev Fort Collins CO 80524 United States

Biodiversity and Crop Improvement International Center for Agricultural Research in the Dry Areas Rabat BP6299 Morocco

Bioinformatics and Information Technology Leibniz Institute of Plant Genetics and Crop Plant Research Seeland Saxony Anhalt 06466 Germany

Brandon Research and Development Centre Agriculture and Agri Food Canada Brandon Manitoba R7A 5Y3 Canada

Cell and Molecular Sciences The James Hutton Institute Dundee Scotland DD2 5DA UK

Centre de Recherche Et d'innovation Sur Les Végétaux Université Laval Québec G1V 0A6 Canada

Centre of Plant Structural and Functional Genomics Institute of Experimental Botany Czech Academy of Sciences Olomouc CZ 77900 Czech Republic

Cereal Crops Improvement Research Unit USDA ARS Fargo ND 58102 United States

Cereal Crops Research Unit USDA ARS Madison WI 53726 United States

Cereal Disease Laboratory USDA ARS Saint Paul MN 55108 United States

Cluster of Excellence on Plant Sciences Düsseldorf North Rhine Westphalia 40225 Germany

Corn Insects and Crop Genetics Research Unit USDA ARS Ames IA 50011 United States

Crop Plant Genetics Institute of Agricultural and Nutritional Sciences Martin Luther University of Halle Wittenberg Halle Saxony Anhalt 06120 Germany

Département de Phytologie Université Laval Québec G1V 0A6 Canada

Department of Agricultural and Food Sciences University of Bologna Bologna 40127 Italy

Department of Agricultural Food and Nutritional Sciences University of Alberta Edmonton AB T6G 2P5 Canada

Department of Agronomy and Plant Genetics University of Minnesota Twin Cities Saint Paul MN 55108 United States

Department of Agronomy Zhejiang University Hangzhou Zhejiang 310029 China

Department of Crop and Soil Science Oregon State University Corvallis OR 97331 United States

Department of Crop and Soil Sciences Washington State University Pullman WA 99164 6420 United States

Department of Field Crops Faculty of Agriculture University of Çukurova Sarıçam Adana 1250 Turkey

Department of Frontier Research and Development Kazusa DNA Research Institute Kisarazu Chiba 292 0818 Japan

Department of Integrated Plant Protection Agrotest Fyto Ltd Kroměříž CZ 767 01 Czech Republic

Department of Plant Pathology Entomology and Microbiology Iowa State University Ames IA 50011 United States

Department of Plant Pathology University of Minnesota Twin Cities Saint Paul MN 55108 United States

Department of Plant Sciences North Dakota State University Fargo ND 58102 United States

Department of Primary Industries and Regional Development Government of Western Australia Perth WA 6151 Australia

Department of Soil and Crop Sciences Texas A and M AgriLife Research Dallas TX 75252 United States

Department of Vegetables and Field Crops ARO Volcani Center Rishon LeZion 7505101 Israel

Division of Plant Sciences The University of Dundee Dundee Scotland DD2 5DA UK

Faculty of Agriculture Setsunan University Hirakata Osaka 573 0101 Japan

Genebank Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Seeland Saxony Anhalt 06466 Germany

Genetic Resources Unit International Center for Agricultural Research in the Dry Areas Praha 15000 Czech Republic

Global Crop Diversity Trust Bonn North Rhine Westphalia 53113 Germany

Halle Jena Leipzig German Centre for Integrative Biodiversity Research Leipzig Saxony 04103 Germany

Institut de Biologie Intégrative et des Systèmes Université Laval Québec G1V 0A6 Canada

Institute for Resistance Research and Stress Tolerance Julius Kühn Institute Quedlinburg Saxony Anhalt 06484 Germany

Institute of Agricultural and Nutritional Sciences Martin Luther University Halle Wittenberg Halle Saxony Anhalt 06120 Germany

Institute of Crop Science National Agriculture and Food Research Organization Tsukuba Ibaraki 305 8602 Japan

Institute of Experimental Botany Centre of Plant Structural and Functional Genomics Olomouc 779 00 Czech Republic

Institute of Plant Genetics Heinrich Heine Universität Düsseldorf Düsseldorf North Rhine Westphalia 40225 Germany

Institute of Plant Science and Resources Okayama University Kurashiki Okayama 710 0046 Japan

Leibniz Institute of Plant Genetics and Crop Plant Research Seeland Saxony Anhalt 06466 Germany

Minnesota Supercomputing Institute University of Minnesota Twin Cities Minneapolis MN 55455 United States

Plant Breeding and Genetics Section School of Integrative Plant Science Cornell University Ithaca NY 14853 1902 United States

Plant Genome and Systems Biology Neuherberg Bavaria 85764 Germany

Plant Physiology and Genetics Unit U S Arid Land Agricultural Research Center Maricopa AZ 85138 United States

Plant Science Program Biological and Environmental Science and Engineering Division Thuwal 23955 6900 Saudi Arabia

Raw Materials Carlsberg Research Laboratory Copenhagen DK 1799 Denmark

Research Centre for Genomics and Bioinformatics Council for Agricultural Research and Economics Fiorenzuola d'Arda Piacenza 29017 Italy

Roche Information Solutions Roche Diagnostics GmbH Penzberg Bavaria 82377 Germany

School of Agriculture Food and Ecosystem Sciences University of Melbourne Melbourne Victoria 3010 Australia

School of Life Sciences Technical University of Munich Freising Bavaria 85354 Germany

School of Plant Sciences and Food Security Tel Aviv University Tel Aviv 69978 Israel

Shandong Academy of Agricultural Sciences Crop Research Institute Jinan Shandong 250100 China

The University of Adelaide Adelaide SA 5064 Australia

Western Crop Genetics Alliance Food Futures Institute School of Agriculture Murdoch University Murdock WA 6150 Australia

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