The Use of different genetic markers to investigate the genetic distinctiveness of the Sardinian wild boar population

The Sardinian wild boar is believed to inhabit the island since the Early Neolithic and is currently recognized as a different subspecies ( Sus scrofa meridionalis ), but after the Second World War translocations of non-native wild boars have been reported. To identify the current status of the genetic diversity of the Sardinian wild boar population, we compared genetic diversity of the wild boar population throughout Europe with a sample of domestic pigs using three different classes of molecular markers: (1) 411-bp sequences of the D-loop region of the mitochondrial DNA, (2) 16 autosomal microsatellites, (3) genome wide scan of 60,000 SNPs (60KSNPs Illumina Beadchip). D-loop data showed that the Sardinian population shares a mtDNA lineage only present here and in peninsular Italy, with a high percentage of private haplotypes. Microsatellite data showed a clear genetic divergence of the population from all mainland populations (F ST = 0.065) and from domestic pigs (F ST = 0.074). A sharp genetic structure was also found within the island. SNP data confirmed the genetic distinctiveness of the Sardinian population from both other wild boars (F ST = 0.081) and domestic pig breeds (F ST = 0.130). Both microsatellites and SNPs highlighted a signature of moderate and localized genetic introgression from mainland wild boars (both Italian and European) and from local domestic breeds. Our results demonstrate that the Sardinian wild boar population still shows significant divergence at both mitochondrial and nuclear loci , supporting its classification as a different subspecies and stimulating further investigations on possible genetic effects of local selective forces.