Wild plants can contribute valuable genes to their domesticated relatives1. Fertility barriers and a lack of genomic resources have hindered the effective use of crop-wild introgressions. Decades of research into barley's closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes2. Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster that has been implicated in diverse immune responses in wheat and barley.

Centre for Crop and Food Innovation Food Futures Institute Murdoch University Murdoch Western Australia Australia

Crop Plant Genetics Institute of Agricultural and Nutritional Sciences Martin Luther University Halle Wittenberg Halle Saale Germany

Department of Soil and Crop Sciences Texas A and M University College Station TX USA

German Centre for Integrative Biodiversity Research Halle Jena Leipzig Leipzig Germany

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

Julius Kühn Institute Federal Research Centre for Cultivated Plants Institute for Resistance Research and Stress Tolerance Quedlinburg Germany

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Seeland Germany

PGSB Plant Genome and Systems Biology Helmholtz Center Munich German Research Center for Environmental Health Neuherberg Germany

School of Life Sciences Technical University Munich Freising Germany

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

Texas A and M AgriLife Research Center at Dallas Texas A and M University System Dallas TX USA

The Institute for Cereal Crops Research Tel Aviv University Tel Aviv Israel

UMR AGAP Institut Univ Montpellier CIRAD INRAE Institut Agro Montpellier France

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