A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum

Wild plants can contribute valuable genes to their domesticated relatives. 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 genes. Here, we construct a pangenome of bulbous barley comprising ten haplotype-resolved genome sequence assemblies. 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 implicated in diverse immune responses in wheat and barley.