Genome-wide detection of selection signatures in native anatolian goat breeds

Native Anatolian goat breeds are genetic resources shaped by traditional management, selection, and adaptation to diverse environments.

This study aimed to identify selection signatures in five goat breeds raised in Türkiye: Ankara, Damascus, Honamli, Kil, and Kilis.

A total of 192 goats were genotyped using the Axiom Goat Genotyping Array containing 59,795 SNP markers. Genome-wide selection signatures were investigated using three complementary haplotype-based statistics: the integrated haplotype score (iHS), the integrated haplotype homozygosity pooled score (iHH12), and the number of segregating sites by length (nSL).

Across all analyses, 2,960 non-redundant gene-method-breed records were identified, corresponding to 2,385 unique candidate genes. The three methods revealed overlapping but complementary signals. iHS highlighted regions associated with production, pigmentation, growth, reproduction, and immunity; iHH12 identified a smaller set related to pigmentation, epithelial biology, immunity, metabolism, and reproduction; whereas nSL detected the broadest set, including regions linked to growth, lactation, lipid metabolism, pigmentation, immunity, reproduction, and vascular development. Repeatability analysis prioritized 276 core genes, 83 strong core genes, and 23 robust core genes recurrent across methods and breeds. Functional enrichment analysis highlighted melanogenesis, endocytosis, phosphatidylinositol signaling, Hippo signaling, calcium signaling, synaptic processes, and cytoskeletal regulation.

These findings provide genomic resources for validation, conservation, and sustainable management.