Genomic evaluation of the Italian shepherd dogs

Dogs have provided great help to shepherds since ancient times, either by protecting or driving the flock. These distinct roles led to the separation of shepherd dogs in livestock guardians (LG) and herding dogs (HD). The constant selection conducted by shepherds and breeders to improve the skills of their dogs originated several breeds, with distinct morphology and behaviour. Given the importance of pastoralism, it is not surprising that Italy counts many local shepherd dog breeds spread across the peninsula. In this study we investigate these breeds from a genomic perspective and identify selection signatures differentiating between LG and HD. Canine 230K SNPChip, updated to CanFam3.1, was used to genotype 134 shepherd dogs. The LG group consisted of 52 dogs of 4 breeds (Maremma sheepdog, Mannara dog, Pastore della Sila, and Fonni’s dog), whereas the HD group consisted of 82 dogs from 5 breeds (Pastore d’Oropa, Pastore apuano, Bergamasco shepherd, Pastore della Lessinia e del Lagorai, and Lupino del Gigante). Commonly used thresholds for quality control were applied (QC) and breed sample sizes were balanced. We compared LG and HD with Wright’s fixation index (FST) and single-SNP cross-population extended haplotype homozygosity (XP-EHH). The top 1% markers for FST and XP-EHH values were considered as relevant. The filtering stage retained 120 836 SNPs and 99 dogs (42 LG and 59 HD). The top 1% of FST (0.24-0.54) and the top 1% of XPEHH (2.72-4.97) had 65 SNPs in common, mapping on 49 different genes. The most intense signals located on chromosomes 6, 9, and 21. A gene-level analysis showed that 8 genes are associated to human eye disorders similar to those that Border collie and its related breeds are prone to develop. Other 8 genes play a role in the nervous system development or functionality. Finally, 20 genes are implicated in behaviour regulation and dog domestication. In this study we reveal genomic traces of the differentiation of Italian LG and HD dog breeds for the first time. The identified genes are related to potentially relevant pathways throughout the selection and the differentiation of these breeds and deserve further investigation to confirm their role in this process.