Genomic characterisation and diversity assessment in endangered Italian sheep breeds

Despite the growing diffusion of some cosmopolite specialized breeds, several autochthonous populations are still reared in marginal areas of Italy. Today, many of these populations encounter the threat of extinction due to factors such as small population size, geographic isolation, limited economic viability, and declining interest in breeding. Assessing their genetic diversity is important to enhance these breeds and their unique traits. Although the Italian ovine diversity has been already investigated, this work aimed to explore the genomic structure of endangered local sheep breeds, never analyzed before, to provide information on their conservation status, essential for managing their genetic variability. A total of 164 animals (15-30 per breed) belonging to eight breeds (Cornella Bianca, Cornigliese, Garfagnina, Nostrana, Pecora dell’Amiata, Pomarancina, Turchessa and Zerasca) were genotyped with the Illumina OvineSNP50 v3 BeadChip array. The raw data were integrated with genotypes from 25 other Italian breeds that had been previously characterized. A total of 824 individuals genotyped for 38,723 markers were used for the analysis. Moderate levels of heterozygosity were observed among the studied populations. Coefficient of inbreeding varied from 0.015 in Zerasca to 0.049 in Cornella Bianca. Multi-dimensional scaling, admixture, and Treemix analyses consistently highlighted the separation of populations based on their genetic origin or geographical proximity between breeding areas. The endangered breeds showed more spread clusters and different levels of admixture. Some breeds (Cornella Bianca, Zerasca and Garfagnina) shared genetic ancestry with Leccese breed. Nostrana showed an internal substructure probably linked to different family lines. Our study provides, for the first time, a consistent overview of population structure, genetic diversity and inbreeding of minority Italian sheep breeds. They highlight the need for a careful monitoring of these populations in accordance with their status of endangered breeds. In this regard, genomic information may significantly contribute to the optimal management of these small populations.