Selection signatures and inbreeding: exploring genetic diversity in five native horse breeds.
Authors: Asti Vittoria, Summer Andrea, Ablondi Michela, Sartori Cristina, Giontella Andrea, Pilastro Valeria, Mecocci Samanta, Cappelli Katia, Mancin Enrico, Oian Angelica, Mantovani Roberto, Capomaccio Stefano, Sabbioni Alberto
Journal: BMC veterinary research
Summary
# Editorial Summary Five native Italian horse breeds—Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse—have been shaped distinctly by natural and artificial selection, yet face ongoing challenges from population decline and shifting breeding purposes. Researchers genotyped 1,498 horses across these breeds using genomic SNP analysis, calculating inbreeding coefficients and identifying runs of homozygosity (ROH) to map selection signatures and candidate genes. Inbreeding levels varied considerably, with FROH values ranging from 0.15 to 0.23; Bardigiano and Haflinger showed highest coefficients due to intensive selective breeding, whilst the remaining three breeds demonstrated broader genetic diversity. Twenty-three ROH islands distributed across 12 chromosomes—particularly on Equine Chromosome 3—overlapped with 83 quantitative trait loci and 76 genes involved in morphology and health, with notably strong associations between ROH patterns and disease resistance traits such as osteochondrosis and hoof integrity in the heavier breeds. These findings provide breeders with actionable genomic data to balance preservation of breed-defining characteristics against maintaining genetic diversity and health standards, particularly relevant given that selection signatures surrounding coat colour genes (MC1R and ASIP) and health-related loci could inform more nuanced breeding strategies across these populations.
Read the full abstract on PubMed
Practical Takeaways
- •Breeders of Bardigiano and Haflinger horses should monitor inbreeding levels closely and consider outcrossing strategies, as these breeds show higher inbreeding coefficients that may limit genetic diversity.
- •Maremmano, Murgese, and Italian Heavy Draught Horse breeds maintain broader genetic diversity and may serve as valuable genetic resources for improving other native breeds while maintaining health and morphological traits.
- •Understanding selection signatures linked to osteochondrosis and hoof health can guide targeted breeding decisions to maintain disease resistance while preserving breed characteristics.
Key Findings
- •Genomic inbreeding coefficients (FROH) ranged from 0.15 to 0.23 across five Italian native breeds, with Bardigiano and Haflinger showing highest values due to selective breeding.
- •23 runs of homozygosity (ROH) islands identified across 12 chromosomes, with 83 overlapping quantitative trait loci associated with morphology and health traits.
- •Health-related traits including osteochondrosis and hoof health were linked to ROH patterns, particularly in cold-blooded breeds, indicating selection for disease resistance.
- •Selection signatures near MC1R and ASIP genes confirmed artificial selection for coat color, especially in Haflinger and Italian Heavy Draught Horse breeds.