Hordeum I genome unlocks adaptive evolution and genetic potential for crop improvement

Crop wild relatives (CWRs) are invaluable for crop improvement. Among these, Hordeum I-genome species exhibit exceptional tolerance to alkali and salt stresses. Here we present a chromosome-scale genome assembly of Hordeum brevisubulatum (II, 2n = 2x =14) and genome resequencing of 38 diploid germplasms spanning 7 I-genome species. We reveal that the adaptive evolution of the H. brevisubulatum genome is shaped by structural variations, some of which may contribute to its adaptation to high alkali and salt environments. Evolutionary duplication of the stress sensor-responder module CaBP-NRT2 and the horizontally transferred fungal gene Fhb7 were identified as novel alkaline–saline tolerance mechanisms. We also demonstrate the potential of the Hordeum I genome in crop breeding through the newly synthesized hexaploid Tritordeum (AABBII) with enhanced alkaline–saline tolerance. Our study fills critical gaps in Hordeum genomics and CWR research, advancing introgression of CWR resources into current crops for sustainable agriculture. The authors present a reference genome for Hordeum I-genome species. This work unravels genomic features that drive adaptation to salt and alkali environments and could aid in improving crop resilience.