The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds

SIMPLE SUMMARY: Shepherd and hunting dog breeds have distinct physical and behavioural characteristics due to their specialized roles. To understand the genetic basis of these differences, we compared the genomes of various Italian shepherd and hunting dog breeds. Our study involved analysing SNP data from 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We examined the genetic makeup, population structure, and relationships of these breeds and compared shepherd and hunting dogs with three complementary techniques. The results clearly showed that there are significant genetic differences between shepherd and hunting dogs. Specific regions of the genome were identified, containing genes associated with domestication, behavioural traits such as aggressiveness and gregariousness, and physical attributes including size, coat colour, and texture. This research provides valuable insights into the genetic factors contributing to the diverse characteristics observed in Italian hunting and shepherd dogs. Further investigation is warranted to explore the implications of these findings for dog health and breeding practices. ABSTRACT: Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: F(ST), XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.