Selection signatures and inbreeding: exploring genetic diversity in five native horse breeds

Horses have undergone extensive natural and artificial selection, shaping the diversity of breeds observed today. Native Italian breeds present unique traits influenced by natural selection, such as adaptation to harsh climates, or hoof strength, but face challenges due to population declines and the reduction of their original breeding purpose. This study focuses on five local Italian breeds: Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse, to understand how selection has shaped their populations. A total of 1620 individuals were genotyped with a medium-density SNP chip and remapped to EquCab3. After quality control, where data were filtered based on missing genotypes per SNP (> 0.10) and missing SNPs per sample (> 0.10), 1498 horses and 54,825 SNPs remained for analysis. Population structure and runs of homozygosity (ROH) were identified, and genomic inbreeding coefficients were calculated based on ROH coverage of autosomal SNPs. ROH islands shared by >= 70% of horses were identified as selection signatures, and candidate genes within these regions were annotated. The inbreeding coefficient (FROH) ranged from 0.15 to 0.23, with Bardigiano and Haflinger showing the highest values probably due to selective breeding, while Maremmano, Murgese, and Italian Heavy Draught Horse displayed lower FROH, reflecting a broader diversity. ROH islands were identified on 12 chromosomes, with 23 islands distributed among breeds. Cold-blooded breeds (Bardigiano, Haflinger, and Italian Heavy Draught Horse) showed the majority, particularly on Equine Chromosome 3 (ECA3). These islands overlapped with 83 quantitative trait loci (QTLs) and 76 genes associated with morphology and health. Health-related traits such as osteochondrosis and hoof health were linked to ROH patterns, particularly in Bardigiano and Haflinger, highlighting selection for disease resistance. Signature of selections were found in the proximity of MC1R and ASIP genes likely due to their role for coat color; especially in the Haflinger and Italian Heavy Draught Horse the genotype frequency of the BIEC2_816499 SNP which is in the vicinity of the causative mutation for chestnut coat color is due to linkage disequilibrium between the two. In conclusion, this study offered valuable insights that breeders could utilize to make sound decisions. This issue would ensure the maintenance of breed genetic diversity, and the preservation and improvement of the breed's distinct traits and health standards.