Genome-wide diversity and runs of homozygosity in the “Braque Français, type Pyrénées” dog breed

Abstract Objective Braque Français, type Pyrénées is a French hunting-dog breed whose origin is traced back to old pointing gun-dogs used to assist hunters in finding and retrieving game. This breed is popular in France, but seldom seen elsewhere. Despite the ancient background, the literature on its genetic characterization is surprisingly scarce. A recent study looked into the demography and inbreeding using pedigree records, but there is yet no report on the use of molecular markers in this breed. The aim of this work was to genotype a population of Braque Français, type Pyrénées dogs with the high-density SNP array to study the genomic diversity of the breed. Results The average observed (\(H_O\)) and expected (\(H_E\)) heterozygosity were 0.371 (\(\pm \,0.142\)) and 0.359 (\(\pm \,0.124\)). Effective population size (\(N_e\)) was 27.5635 runs of homozygosity (ROH) were identified with average length of 2.16 MB. A ROH shared by \(75\%\) of the dogs was detected at the beginning of chromosome 22. Inbreeding coefficients from marker genotypes were in the range \(F_{IS}=[-\,0.127,0.172]\). Inbreeding estimated from ROH (\(F_{ROH}\)) had mean \(0.112\,(\pm \,0.023\)), with range [0.0526, 0.225]. These results show that the Braque Français, type Pyrénées breed is a relatively inbred population, but with still sufficient genetic variability for conservation and genetic improvement.