ArticleMammalian genome : official journal of the International Mammalian Genome Society2026
Adaptive landscape and genetic divergence of Karnah sheep revealed by selection scans across multiple ovine breeds.
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Abstract
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 F
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