Adaptive landscape and genetic divergence of Karnah sheep revealed by selection scans across multiple ovine breeds.

Indigenous sheep constitute vital reservoirs of adaptive genetic diversity, yet their genomic signatures of adaptation are poorly understood. The present study provides a comprehensive genomic characterization of the endangered Karnah sheep (Ovis aries) native to North Kashmir, India. A total of 41,812 high-confidence SNPs were used across 266 individuals representing nine geographically and functionally diverse breeds (i.e., Karnah, Garole, Deccani, Changthangi, Tibetan, Australian Merino, Rambouillet, Suffolk, and Texel). Population structure analyses revealed pronounced genetic stratification with PC1-PC3 explaining 13.81% variance, separating Asian indigenous clusters (high-altitude vs. lowland) from European-derived wool and mutton populations. This pattern was consistently supported by ADMIXTURE (optimal K value of 8) and neighbor-joining phylogenetic analysis, identifying two deeply rooted clades. Genome-wide nucleotide diversity (π) estimates indicated relatively uniform diversity across populations, with Australian Merino exhibiting the highest diversity (106% of the mean), followed by Karnah (102%), while Garole showed the lowest (93%). Pairwise FST values ranged from 0.03 to 0.188, reflecting moderate genetic differentiation, with the lowest differentiation observed between Changthangi and Tibetan breeds and the highest between Garole and European breeds. Selection signature analyses revealed strong adaptive signals in Karnah sheep. Intra-population iHS analysis (|iHS| > 3) identified key candidate genes such as RELN, ADIPOQ, and RAP1B associated with environmental resilience, metabolism, and reproduction. Cross-population XP-EHH and FST analysis further highlighted genes involved in lipid metabolism (ATP8B2, ELOVL1), calcium signaling (CACNA1C), and immune response (NFKB2, HS6ST3), indicating adaptive divergence driven by climatic and ecological pressures. Functional enrichment supported pathways related to immunity, metabolism, and reproduction. Collectively, these findings provide a robust genomic framework for understanding adaptive evolution in Karnah sheep and offer valuable insights for conservation and climate-resilient breeding strategies.