Whole-Genome Resequencing Reveals Deep Genomic Differentiation and Highly Differentiated Segments Between a Composite Domestic Cattle Population and Yak from the Ili River Valley and Other Xinjiang Regions

The Ili River Valley and adjacent Xinjiang regions contain introduced cattle, local cattle, and yak and therefore provide a useful regional system for examining cattle–yak genomic differentiation. Using whole-genome resequencing data from 79 individuals, we analyzed Angus (ANG), Simmental (SIM), Holstein (HOL), Xinjiang Brown Cattle (XH), Kazakh Cattle (KAZ), Altay White-headed Cattle (AWH), and yak (WY). The six domestic cattle groups were merged into a composite domestic cattle group (PTN, n = 69) and compared with WY (n = 10). Sequencing generated 2996.28 Gb of raw data and 2939.56 Gb of clean data. Alignment to the Bos taurus ARS-UCD1.2 reference genome yielded mapping rates of 96.71–99.78% and depths of 5.98×–17.26×. Genome-wide PTN-WY comparisons showed extremely high differentiation: the median weighted F_ST was 0.846 and the 95th percentile was 0.943. The joint F_ST–π scan identified 832 candidate highly differentiated windows and 533 unique ENSBTAG gene IDs, whereas the low-differentiation set contained only five windows and three genes. The longest contiguous highly differentiated segments were located on chromosomes 26, 29, 8, 21, and 7. WY had the highest median Tajima’s D (1.173) and the slowest LD decay, while KAZ had the lowest median Tajima’s D (0.345) and the fastest LD decay. Treemix supported non-tree-like covariance components, and PSMC indicated broadly similar deep-time demographic profiles across individuals. Overall, the dominant genomic signal between PTN and WY is deep phylogenetic divergence, with locally enhanced highly differentiated segments superimposed on this background. These segments were enriched for functions and pathways related to reproductive behavior, neuroendocrine regulation, circadian rhythm, and membrane transport, but they are not interpreted here as recent within-species selective sweeps. The results provide a cautious regional framework for conservation and breeding of bovine genetic resources in Xinjiang.