Do we have breeding for performance and distinctiveness in traditional horse local breeds

Today, horse local breeds traditionally used in agriculture face the challenge to modernize their breeding goals to meet current market demand while preserving their distinctive characteristics; otherwise, extinction is a solid possibility. Genetic diversity management is a powerful tool to prevent this risk. Nevertheless, by improving the breed’s economic value through selective breeding might contribute as well to enhance its sustainability in the long term. The Italian equine gene pool is rich and diversified in more than 20 native breeds. Thus, this study aimed to evaluate the presence of signatures of selection in the five most representative Italian breeds, based on population size. Genotype data (GGP Equine 70k® SNP chip) of 915 horses from Bardigiano, Haflinger, Maremmano, Murgese and Italian Heavy Draught breed were analysed. Two methods were applied: Pairwise Fixation Index (Fst) and Runs of Homozygosity (ROH). The pairwise Fst was calculated in the R package SNPRelate and ROH island discovery (as ROH shared in over 70% of the horses within breed) was performed in the R package DetectRUNS. The pairwise Fst ranged between 0.06 to 0.11 showing for most comparisons Fst values above 0.50 for specific SNPs, which might underline regions potentially linked with the distinctive features of each breed. In all the breeds ROH longer than 16 Mb were found. A total of 32 ROH islands were detected: 19 were present in one breed only, whereas the others were shared among at least two breeds. Several mapped to known quantitative trait loci for morphological traits (e.g. body size and coat colour), disease susceptibility and gaits related traits. Further research is ongoing to unravel if those signs of selection play a role in keeping the traditional features of each breed while helping the conversion from agricultural uses to riding purposes.