Genetic variability and population structure of Southern Italy sheep breeds

Different native sheep breeds are raised in the southern regions of Italy. These breeds display interesting traits such as a complete adaptation to the local Mediterranean environment, a peculiar morphology and history and a particular taste of their products. The aim of the study was to characterize sheep biodiversity in Southern Italy at DNA level in order to allow efficient conservation strategies and to develop protocols of genetic traceability for sheep products. A total of 743 individuals from seven autochthonous breeds (Altamurana, Bagnolese, Comisana, Gentile di Puglia, Laticauda, Leccese and Sarda) were sampled in different flocks avoiding relatives. Genotypes were assessed for 19 microsatellites and for 104 SNP loci. Allele richness at STR loci ranged from 8.8 (Sarda) to 11.6 (Gentile di Puglia), while private allele richness was higher in Leccese (0.53) and lower in Sarda (0.32). A moderate level of inbreeding (Fis ranging from 0.147 in Gentile to 0.05 in Sarda) was observed with STR markes while Fis values were lower when considering SNP loci ; this discrepancy suggests the existence of null allele at STR loci. Overall FST values were similar for SNP and STR markers (0.04916 and 0.4894, respectively) and indicate a moderate level of breed differentiation. Considering pair-wise FST values, Altamurana and Sarda resulted to be the most distant and differentiated breeds. Structure analysis highlighted (at k 10), the the partitioning of genetic variability not only among breeds but also notably among flocks. The findings of this study can be exploited to implement effective policies to protect sheep biodiversity as well as protocols to authenticate sheep products.