A haplotype-based evolutionary history of barley domestication

Abstract

Barley, one of the earliest domesticated crops, has a complex domestication history marked by mosaic genomic ancestry rather than a single origin. Using a haplotype-based framework, we analyzed 628 modern and 23 ancient barley genomes to trace the origins and distribution of haplotypes across wild and domesticated populations. Our findings indicate an early founder population in the Fertile Crescent, shaped through prolonged pre-domestication cultivation and subsequent gene flow. We also investigated Hordeum agriocrithon, a group of morphologically intermediate barley forms from Asia. Genomic evidence shows these are not direct progenitors but independent hybrids between wild and domesticated barley. While H. agriocrithon is not central to domestication, its existence highlights the dynamic and bidirectional nature of gene flow, underscoring challenges in identifying adaptive loci and offering avenues for future research into crop evolution.