Whole-genome sequencing of 1 363 individuals reveals population structure and local adaptation of Xinjiang indigenous sheep

Indigenous sheep breeds in Xinjiang, China, display marked phenotypic diversity across heterogeneous environments, yet their population structure and evolutionary history of key traits remain incompletely resolved. We analyzed whole-genome resequencing data from 1 363 individuals representing 14 indigenous Xinjiang sheep populations. Population genomic analyses revealed three major genetic clusters. Cele Black and Karakul sheep formed two distinct lineages that diverged from the main cluster approximately 2 000 years ago, whereas the remaining breeds separated more recently, approximately 1 000 years ago. Trait-focused selection scans identified candidate loci associated with reproductive seasonality, coat color, and fat-rumped morphology. Comparisons between year-round and seasonal breeders showed strong selection at TSHR in year-round estrus breeds. Fine mapping prioritized a candidate regulatory variant (g. 90612698T > G), which was enriched in year-round breeders and associated by eQTL analysis with reduced TSHR expression in thyroid tissue. Coat-color comparisons identified a high-frequency KIT variant (g.70935444 G > A) in Cele Black and Karakul sheep, with allele-frequency trajectory inference indicating a recent rise approximately 400 years ago. For fat-rumped sheep, ancestral recombination graph reconstruction traced the genealogical history of a TBXT-associated variant (g.88882077 C > A), whose derived allele increased in frequency approximately 1 800 years ago. Overall, our results provide a genome-wide view of genetic diversity and demographic history in Xinjiang sheep and highlight candidate variants underlying economically important traits, offering resources for conservation and molecular breeding.