Genome-wide selective sweep analysis in high-altitude Changthangi goats reveals candidate genes for pashmina fiber production.

Domestic goats (Capra hircus) are vital to global agriculture, with over one billion animals supporting smallholder farmers worldwide. Among goat breeds, the Changthangi goat, native to the trans-Himalayan region of Ladakh, produces pashmina, one of the finest natural fibers (12-16 μm diameter), renowned for its softness and insulation. This study presents the first comprehensive whole-genome comparative analysis between high-altitude pashmina-producing Changthangi goats and lowland Jamunapari goats to elucidate the genetic basis of superior fiber traits. Genome-wide selection signature analyses, including Tajima's D, nucleotide diversity (π), CLR, iHS, F, and XP-EHH, revealed 2,113 and 839 candidate genes under intra- and inter-population selection, respectively. We identified several candidate genes under selection in Changthangi goats, including those regulating keratinocyte differentiation (BMP2, SMAD3, WNT9B), extracellular matrix organization (COL1A2, ITGA4), and metabolic adaptation (ADCY4, RPS6KB1). Functional annotation and pathway enrichment using DAVID and KEGG databases highlighted key pathways such as Wnt, BMP/TGF-β, Hedgehog, Rap1, PI3K-Akt, and ECM-receptor interaction, which regulate hair follicle morphogenesis, and fiber structure. Gene interaction networks highlighted hub genes (FGF5, SMAD7, COL1A2) critical for fiber traits. Our findings provide novel insights into the genomic signatures underlying elite pashmina production, offering targets for marker-assisted breeding to enhance fiber yield and fineness.