Fine-scale assessment of ROH patterns and genomic inbreeding in diverse horse breeds using two SNP array densities.
Authors: Moghbeli Damane Moslem, Ayatollahi Mehrgardi Ahmad, Esmailizadeh Ali, Momen Mehdi
Journal: BMC veterinary research
Summary
# Editorial Summary Runs of homozygosity (ROH)—extended chromosomal segments inherited in identical form from common ancestors—provide a precise genomic measure of inbreeding and autozygosity that conventional pedigree analysis often misses, particularly in horse populations shaped by geographical isolation and intensive selection. This research examined ROH patterns across diverse horse breeds using two different SNP array densities to establish whether high-density genotyping offered meaningful advantages over standard arrays for detecting inbreeding levels and characterising population structure. The team's fine-scale assessment revealed that whilst both array types identified inbreeding signatures, higher-density SNP panels captured shorter ROH segments and provided more granular detail on recent versus historical inbreeding events—critical distinctions for understanding whether elevated homozygosity stems from recent close breeding or accumulated selection across generations. For breeding programmes and stud book management, these findings underscore the value of high-resolution genomic screening when designing pedigree strategies to maintain genetic diversity, particularly in rare or geographically confined breeds where the risk of cumulative inbreeding depression (reduced fertility, athleticism, and health) is pronounced. Farriers, veterinarians, and nutritionists working with at-risk populations should be aware that genomic inbreeding coefficients derived from ROH analysis offer a more reliable predictor of individual fitness and performance potential than traditional calculations alone.
Read the full abstract on PubMed
Practical Takeaways
- •Use genomic ROH analysis to make informed breeding decisions that preserve genetic diversity and reduce inbreeding depression in your breeding program
- •Understanding ROH patterns helps identify which breeds or bloodlines carry higher inbreeding loads, enabling strategic outcrossing decisions
- •Implement genomic inbreeding assessment as part of modern breeding management to maintain population fitness and performance across generations
Key Findings
- •Runs of homozygosity (ROH) analysis provides accurate assessment of genomic inbreeding and autozygosity in horse populations
- •ROH patterns reveal population diversity, demographic history, and intensity of selection across diverse horse breeds
- •Fine-scale assessment using two SNP array densities enables detection of both recent and ancient inbreeding events