Genetic diversity is a key factor for both adaptation and response to selection. The loss of genetic diversity causes a decrease in individual fitness, and it has a dramatically negative effect on population lifespan in the long term. This study aimed at exploring the genetic diversity at pedigree level of the Bardigiano horse breed, which is a native breed from Italy shaped for living in rural areas. In 1977, the Bardigiano studbook was founded to preserve the breed and for improving its use for riding and draft purposes. Pedigree data contained 9,469 horses, of which 3,416 were alive. Demographic and genetic parameters were estimated on subpopulations to evaluate potential genetic diversity differences among breeding and nonbreeding animals, and animals showing different breeding values (EBVs) for an index combining 18 conformation traits. Throughout the studied period, inbreeding steadily increased, reaching in the last birth year cohort a mean value equal to 0.10. The rate of inbreeding per generation, assuming a mean generation interval of 8.74 years, was equal to 1.64%. Moreover, significant differences on both average relatedness and inbreeding among horses with high and low EBVs were shown. Our study unravelled the state of genetic diversity in the Bardigiano breed, highlighting that breeding strategies for optimizing the contribution of breeding animals in the coming generations are needed to ensure long-term survival of the Bardigiano horse breed.

Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.

Horses are nowadays mainly used for sport and leisure purposes, and several local breeds, traditionally used in agriculture, are exposed to the risk of extinction. The long‐term survival of local horse breeds depends on strategies to both monitor their genetic diversity and to find their sustainable role in the equine market. Thus, several local horse breeds need to adapt their breeding objective to allow a modernization process. The Bardigiano is an example of such horse breeds; we, therefore, studied the existing evaluation protocol from a genetic standpoint to assess the protocol's suitability to convert the Bardigiano from an agricultural to a riding horse. To this end, we estimated genetic parameters for four conformation measurements, ten grading traits and 23 linear traits. For conformation measurements, the heritabilities ranged from 0.31 for cannon bone circumference to 0.63 for height at withers. For conformation and attitude grading traits, the highest heritability (0.34) was estimated for development and the lowest (0.09) for gaits. The heritabilities for linear traits ranged from 0.05 for the leg straightness to 0.32 for the coat colour. Genetic correlations between linear traits and corresponding grading traits varied considerably, ranging from −0.42 to 0.98. This study showed that the current evaluation protocol in the Bardigiano horse is appropriate for genetic evaluation. Genetic parameters estimation can, in turn, be used to develop novel breeding values to help this conversion. Our study paves the way to optimize the Bardigiano horse breeding programme, and it may help several other local horse breeds experiencing similar issues.