Genomic Analysis of the Endangered Fonni’s Dog Breed: A Comparison of Genomic and Phenotypic Evaluation Scores

Simple Summary The Fonni's dog is a local breed selected for livestock and property guarding by Sardinian farmers since ancient times; however, this breed is now at high risk of being lost. The present study analyses the genomic background of 30 Fonni's dogs genotyped with a high-density SNPchip and compares the genomic score obtained by admixture analyses with two morphological scores based on breed typicality and official judges' evaluation. Genomic analyses showed that this breed is close to other shepherd dogs, but at the same time presents a unique genetic signature. All three scores were positively correlated, with higher values between the genomic and typicality scores. The judges' score of the included dogs was a little variable and, therefore, could be improved to better rank dogs and include features that are particular to the breed. A shared vision between breeders and the Italian kennel club, as well as the support of dedicated regional programs, are fundamental in order to recover and preserve the Fonni's dog. The Fonni's dog is an ancient Sardinian breed for livestock and property guarding. In recent years, the number of new registrations to the breeding book has slumped and, thus, this breed risks being lost forever. This work refocuses attention to the Fonni's dog, analysing its genomic makeup and comparing different phenotypical and genetic evaluation scores. Thirty Fonni's dogs were ranked by their general accordance to the breed typicality (typicality score) and to the provisional standard by official judges (judges' score). They were genotyped with a 230K SNP BeadChip and compared with 379 dogs of 24 breeds. Genomically, the Fonni's dogs placed themselves near shepherd dogs and showed a unique genetic signature, which was used to create the genomic score. This score better correlated with typicality (rho = 0.69, p < 0.0001) than the judges' score (rho = 0.63, p = 0.0004), which showed little variability among the included dogs. Hair texture or colour were significantly associated in the three scores. The Fonni's dog is confirmed as a well-distinguished breed, despite being selected mainly for its work abilities. The evaluation criteria used during dog expositions can be improved to increase their variability and include elements typical of the breed. The recovery of the Fonni's dog would be possible only with a shared vision between the Italian kennel club and breeders, and the support of regional programs.