Phenotypic and Genomic Characterization of the Comune di Sicilia Goat: Towards the Conservation of an Endangered Local Breed

SIMPLE SUMMARY: The Comune di Sicilia goat, originating in Sicily (Italy), is in the process of being officially acknowledged as a breed. To better characterize this population, this study examined 78 goats from two locations, recording the goats’ morphological traits and measurements. Moreover, these goats were genotyped using a medium-density SNPchip and compared with goats from 15 different Italian breeds. The study found that the Comune di Sicilia goats have unique physical and genetic characteristics that distinguish them from other breeds in the same area. However, moderate variability was observed, likely influenced by how the goats were chosen by breeders. Additionally, the genomic comparison of goats with different traits led to the identification of genes possibly linked to anotia and wattle presence in goat species. To preserve this breed and avoid problems with inbreeding, a combined approach integrating phenotypic and genomic analyses is warranted. ABSTRACT: The Comune di Sicilia, a local goat breed from Sicily (Italy), is currently undergoing recognition as a distinct breed. This study aims to characterize the population both phenotypically and genomically to advance its recognition process. A total of 78 subjects from two locations were enrolled, and their phenotypic data, including qualitative traits and morphometric measurements of adult animals, were recorded and statistically analyzed. The goats were genotyped using the Illumina 50 k Goat SNPchip, comparing them with 473 goats from 15 Italian breeds. Population structure, phylogenetic relationships, admixture, and genomic inbreeding were analyzed. Additionally, subjects with different morphological traits were compared using F(ST) and runs of homozygosity, leading to the identification of potential candidate genes associated with anotia and wattle presence in goats. The Comune di Sicilia breed exhibited distinctive genomic and phenotypic features, setting it apart from other breeds in the same region. However, moderate variability, possibly influenced by selection practices, was also observed. To ensure the breed’s preservation and prevent excessive inbreeding, a comprehensive approach considering both morphology and genomic background is recommended. This study contributes valuable insights into the genetic peculiarities of the Comune di Sicilia goat, supporting its recognition as a unique and valuable breed.