Genomic ancestry and adaptive signatures in the indigenous Hetian cattle from Xinjiang Province of China revealed by whole-genome sequencing

Abstract

Background Cattle domestication and subsequent breed formation have profoundly shaped agricultural economies and ecological adaptation worldwide. Among these, Chinese indigenous breeds exhibit extensive phenotypic diversity driven by complex admixture histories. Hetian cattle, a native population from the arid Xinjiang Province of China, possess superior traits including drought tolerance and disease resistance. Despite their ecological and agricultural importance, the genomic architecture and adaptive mechanisms underpinning these traits remain poorly characterized. Result To address this gap, we performed whole-genome resequencing of 20 Hetian cattle and integrated comparative analyses with 162 globally representative cattle genomes. We assessed genomic diversity, population structure, and local ancestry using a combination of principal component analysis, admixture modelling, and neighbor-joining phylogenies. Ancestry inference revealed a nearly equal taurine (49.99%) and indicine (50.01%) genetic composition, tracing to an admixture event approximately 38 generations ago. Selection signature analyses using CLR, iHS, and nucleotide diversity metrics identified genomic regions under positive selection associated with immunity (e.g., SLAMF1, CD84), high-altitude adaptation (AGBL4, ALX3), and drought resistance (HNRNPK, XYLT1, ADPGK). Two missense mutations (rs208626726 and rs134151223) within candidate genes may contribute to the physiological resilience of Hetian cattle. Conclusion This study elucidates the genetic basis of local adaptation in Hetian cattle through comprehensive genomic characterization. The identification of key adaptive loci provides valuable insights into the evolutionary history and environmental resilience of this population. These findings contribute to the conservation genomics of Chinese native cattle and inform molecular breeding strategies aimed at improving adaptation and productivity under climate-stressed agroecosystems. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-025-12346-7. Keywords: Adaptive evolution, Cattle domestication, Genomic diversity, Hetian cattle, Indicine–taurine admixture, Local ancestry inference, Missense mutation, Selective sweep analysis