Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data.
Authors: Ablondi Michela, Dadousis Christos, Vasini Matteo, Eriksson Susanne, Mikko Sofia, Sabbioni Alberto
Journal: Animals : an open access journal from MDPI
Summary
# Editorial Summary: Genetic Diversity in the Bardigiano Horse Breed The Bardigiano, an Italian native breed historically essential to agricultural work, now faces the genetic challenges common to many heritage horse populations—declining numbers and reduced diversity that threaten long-term viability. Researchers analysed SNP data from 70,000 genetic markers across Bardigiano horses to quantify genetic erosion and identify genomic regions shaped by selective breeding pressures. The breed's effective population size stands at just 39 individuals, with an average inbreeding coefficient of 0.17; notably, 91% of homozygous segments were relatively short, indicating accumulated inbreeding over many generations rather than recent intensive selection. Eight distinct genomic regions showed strong conservation across more than 70% of sampled animals, with four mapping to known traits including body size, coat colour and disease susceptibility—suggesting these characteristics have been deliberately or inadvertently maintained despite overall genetic loss. For equine professionals managing heritage breeds, these findings underscore both the vulnerability of small breeding populations and the potential for targeted genomic approaches to inform breeding decisions that balance trait preservation with genetic health, particularly when selecting breeding stock for morphology or disease resistance.
Read the full abstract on PubMed
Practical Takeaways
- •Breeding programs for the Bardigiano breed should prioritize genetic diversity management through strategic outcrossing and pedigree analysis to combat the critically low effective population size of 39
- •Elevated inbreeding levels indicate practitioners should monitor offspring for fitness issues and disease susceptibility linked to identified ROH regions affecting morphology and health
- •Conservation efforts should focus on identifying and preferentially breeding horses with minimal contribution to the eight high-frequency ROH islands to restore genetic variation
Key Findings
- •Effective population size (Ne) of Bardigiano breed was 39 horses with decline over time, indicating severe genetic bottleneck
- •Average inbreeding coefficient of 0.17 (SD = 0.03) with 91% of runs of homozygosity ≤2Mbp, suggesting older inbreeding events rather than recent
- •Eight ROH islands shared among >70% of Bardigiano horses, with four mapping to quantitative trait loci for body size, coat color, and disease susceptibility
- •Genome-wide SNP analysis revealed significant loss of genetic variability in this Italian native breed with implications for long-term survivability