Genomic characterization of an Apennine heeling dog population: insights into diversity and conservation

Over centuries, dogs have accompanied human populations during seasonal livestock movements associated with transhumance, contributing to the development of specialized pastoral dog populations. This study focuses on a population of heeling dogs distributed across the Italian Apennines, here referred to as Apennine heeling dogs, traditionally selected by shepherds based on homogeneous morphological and behavioral traits. The aim of the present study was to provide a genome-wide characterization of this population and to investigate its genetic relationships with other shepherd and herding breeds. A total of 16 individuals with documented pastoral ancestry (AppHeelDog) and 6 morphologically similar dogs with uncertain ancestry (AppMorph) were genotyped using a medium-density SNP array and analyzed together with publicly available datasets. The results indicate that the Apennine heeling dog forms a genetically coherent and distinct cluster across all analyses. ADMIXTURE revealed a characteristic ancestry component largely absent in other breeds, while TreeMix indicated a predominantly tree-like evolutionary history with no evidence of recent gene flow. A genomic affinity with continental European herding breeds, particularly German and Belgian Shepherd lineages, was also observed. Despite moderate genetic diversity, the population exhibited substantial genomic inbreeding and a reduced effective population size. The AppMorph group showed partial genetic overlap with the core AppHeelDog population but also evidence of heterogeneity, highlighting the importance of integrating genomic and phenotypic data when defining population boundaries. Overall, this study provides the first genomic evidence supporting the distinctiveness of the Apennine heeling dog and establishes a foundation for its recognition and conservation.