Identification of adaptive selection footprints and adaptation strategies of hulless barley (Hordeum vulgare var. coeleste) on the Qinghai-Tibet Plateau

BACKGROUND: After millennia of cultivation on the Qinghai-Tibet Plateau (QTP), hulless barley has developed remarkable adaptability. Decoding its genomic adaptive variations is crucial for elucidating the mechanisms underlying its plateau adaptation. RESULTS: In this study, Genotyping 500 barley accessions generated 12,151 SNPs, revealing two major groups with geographic subdivisions. QTP barley exhibited lower genetic diversity and slower linkage disequilibrium decay, indicating stronger selection pressures or genetic drift. Gene flow revealed that Central Asia-West Asia wild barley represents the ancestral group, and gene exchange between the two major groups was limited. EigenGWAS and selective sweep analyses identified candidate genes associated with domestication and adaptation. Flowering-related genes were highlighted as potentially critical for adaptation to high altitudes. Importantly, nud and Rpg5 were recurrently detected across multiple adaptive regions. CONCLUSION: A total of 500 barley accessions exhibit obvious population structure, which can be mainly divided into two distinct groups. Among them, hulless barley shows slow linkage disequilibrium decay and has undergone relatively strong selective pressure. Additionally, numerous candidate genes involved in adaptive processes have been identified. These findings elucidate the genetic basis of hulless barley's adaptation to the QTP and underscore genomic signatures associated with environmental resilience and domestication.