Genomic insights on the history and selection trajectories of the Comune di Sicilia goat

Background: The Capra Comune di Sicilia (CCS), also known as Mascaruna, is a Sicilian local goat population first described in 1870 and is currently the focus of a recovery project aimed at its characterization and formal ethnic recognition. To elucidate the ancestral genetic components and selection trajectories of the CCS population, we genotyped 78 CCS goats using the Goat 60 K SNP BeadChip, integrated with genotype data from 1,920 individuals representing 66 goat breeds of Mediterranean and African origin. Results: CCS exhibited relatively high heterozygosity (0.408), and moderate levels of inbreeding (0.04), an estimated effective population size of 185. Genetic ancestry analysis revealed gene flow from Maltese, Girgentana, Rossa Mediterranea and Saanen populations, alongside evidence of putative Greek ancestry shared with most Mediterranean breeds in our dataset, reflecting Sicily’s profound historical and cultural ties with Greece. To better understand the evolutionary trajectories of the CCS population and to explore the potential contribution of Greek goat ancestry, we investigated selection signatures using iHS and ROH analyses. We identified 76 and 31 SNPs intercepting 38 and 12 genes, respectively, under putative selection. Subsequently, we applied XP-nSL and ROH analyses using Greek populations as ancestral references, identifying 21 and 431 SNPs associated with four and 157 genes, respectively, under putative selection. Overall, these selection signature analyses highlighted genes under positive selection related to traits such as milk and meat production, body size and growth, fertility, coat colour, fat deposition, and ear and horn development. Conclusion: Our findings shed light on the historical and genetic distinctiveness of the CCS population, emphasizing its uniqueness and providing critical insights into its genetic background. This information is essential for supporting informed efforts to formally recognize CCS as a distinct and valuable breed.