Uncovering genomic traces of local adaptation and milk production traits in the Comisana Sheep, a Mediterranean dairy breed

Domestic animals provide valuable models for exploring the genetic basis of long-term adaptation to diverse environments over relatively short evolutionary timescales. This study investigates genomic signatures of selection in the Comisana sheep breed (COM), known for its resilience in low-input systems and adaptation to the semi-arid Mediterranean climate. We analysed genotypes from 238 COM individuals, integrating them with data from the Sarda (SAR; N = 138) and Valle del Belice (VDB; N = 125) breeds. Using a combination of extended haplotype homozygosity (EHH)-based and population differentiation-based tests, we identified eight candidate genomic regions under selection in Comisana. Notably, a strong and consistent signal on ovine chromosome (OAR) 2, observed across all methods, encompassed the genes NFIB, FREM1, and ZDHHC21, which are involved in lung development, epithelial integrity, immune regulation, and thermoregulation, traits likely contributing to adaptation in harsh environments. On chromosome 3, three synonymous mutations were detected in the SLC6A15, LEMD3, and XPOT genes, all implicated in tissue repair and defence against pathogens, supporting their role in local adaptation. Other selected regions contained genes associated with milk production. A particularly strong signal on chromosome 6, characterised by a hard selective sweep, likely reflects recent artificial selection driven by structured breeding programmes. Overall, our findings suggest that selection in Comisana sheep targets pleiotropic genes involved in both environmental resilience and dairy performance, underscoring the combined influence of natural and artificial selection in shaping the genomic landscape of Mediterranean dairy breeds.