Skin transcriptome comparison of Changthangi Pashmina and Sirohi goats reveals fibre-barrier and skin remodeling expression signatures

Goat breeds have developed diverse phenotypic characteristics through natural selection and long-term exposure to different environments. In this study, we compared skin transcriptomes from the high-altitude, cold-adapted Changthangi Pashmina goat and the hot, semi-arid-adapted Sirohi goat. To our knowledge, this is the first comparative transcriptomic study of these two contrasting goat breeds, revealing distinct molecular signatures associated with skin biology, fibre production, breed-specific characteristics, and molecular response to contrasting climatic conditions. Differential expression analysis identified 420 significant DEGs (|log2FC| ≥ 1, FDR < 0.05), including 180 genes upregulated in Pashmina and 240 in Sirohi. Changthangi Pashmina goats showed enrichment of keratinization , formation of the cornified envelope , epidermal differentiation , lipid metabolism , and hair-follicle-development processes. Key upregulated genes in Pashmina goats including ASIP , AWAT1 , KLK6 , KRT77 , KRT79 , DGAT2L6 , LIPK , CES3 , CES4A , AADACL3 , TGM5 , and WNT4 were associated with white fibre formation, secondary hair-follicle development, fine-fibre formation, epidermal barrier maturation, lipid-rich skin and coat maintenance, and thermal insulation, features that are central to Pashmina production and survival under the cold, arid, high-altitude environment of Ladakh. Sirohi goats showed significant enrichment of signaling pathways like IL , TNF , chemokine , tyrosine , immune response , inflammatory , oxidative-stress and endocrine processes . These pathway-level changes were supported by upregulation of TYR , TYRP1 , DCT , PMEL , TRPM1 , SOX10 , IL6 , CXCL8 , CXCL10 , PTGS2 , CH25H , ACOD1 , and SLC7A11 . The upregulated genes were consistent with the characteristic dark pigmentation, heat tolerance, immune responsiveness and overall environmental robustness of Sirohi goats. These findings provide a strong foundation for livestock improvement related to fibre quality and climatic adaptation. Validation of these candidates in larger populations may support future breeding strategies for developing goats with better fibre traits, improved performance, and greater resilience to changing environmental conditions.