Genome-Wide Analyses of Breed Differentiation and Candidate Functional Genomic Differentiation in Domestic Dogs

Abstract Domestic dog breeds show extensive phenotypic diversity shaped by recent breed formation, closed breeding, founder effects, genetic drift, and artificial selection. However, how these processes have contributed to genomic differentiation among modern breeds remains incompletely characterized. Here, we integrated genome wide SNP genotype data from more than 5,000 dogs as a global reference dataset and newly genotyped approximately 300 dogs from eight focal breeds to investigate population structure, genomic inbreeding, and breed group differentiation. Genome wide dimensionality reduction and ADMIXTURE analyses revealed clear genetic structuring among modern breeds, with newly genotyped populations clustering with their corresponding public reference breeds. Genomic inbreeding analyses showed that modern purebred dogs generally exhibited elevated FROH compared with village dogs and wolves, and population level FROH was positively correlated with mean pairwise FST. Window based FST scans across selected FCI breed group comparisons identified highly differentiated genomic regions. Functional annotation of candidate genes revealed comparison specific enrichment patterns, including muscle and cytoskeletal terms in some French Bulldog related comparisons, but no uniform functional profile across all breed group contrasts. Finally, we developed compact ancestry informative SNP panels for genetic breed assignment among the eight focal breeds, with the 200 SNP panel providing clear resolution of breed structure in the present dataset. Together, these findings provide a genome wide overview of differentiation among selected dog breeds and identify candidate regions and marker sets for future studies of canine breed history, breed associated morphology, and genotype-based breed assignment.