Angora and Cashmere goats differ in hair follicle biology and fibre traits. To explore the genetic basis of these differences, Whole Genome Sequencing (WGS) of Cashmere, Angora, and non-fibre goats were used to identify divergent selection signatures and allele frequency differences. Cross-population analyses found 5,252 variants differentially selected between Cashmere and non-fibre goats, 2,414 between Angora and non-fibre, and 326 between Cashmere and Angora. Three fibre-related genes, COL14A1, FGF5, and CUX1, showed divergence across all comparisons. Fisher’s exact test on coding variants with high or moderate predicted phenotypic impact identified 735 significant variants in skin-expressed genes showing differing allele frequencies between Cashmere and non-fibre goats, with fewer such variants found between the other groups. These variants likely influence fibre differences among populations. Though their exact effects are unclear, this study advances understanding of fibre goat genetics. © 2025 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

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