Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares.
Authors: Laseca Nora, Molina Antonio, Ramón Manuel, Valera Mercedes, Azcona Florencia, Encina Ana, Demyda-Peyrás Sebastián
Journal: Frontiers in veterinary science
Summary
# Editorial Summary: Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares Selective breeding programmes in equine populations have inadvertently narrowed the genetic base, raising concerns about inbreeding depression and its consequences for reproductive performance—a particular problem in horses where closely related individuals are frequently bred together. Using SNP genotyping and genomic analysis of runs of homozygosity (ROH) in a substantial cohort of Pura Raza Española mares, researchers correlated genome-wide homozygosity with fertility estimated breeding values (EBVs), revealing a modest but significant negative relationship at the whole-genome level (ρ = −0.144) that strengthened considerably when comparing the 10% most and least fertile mares (ρ = −0.241), with the latter group displaying approximately 30% higher average inbreeding coefficients. Notably, 41 genomic "islands" of extreme homozygosity (100-fold enrichment) were identified across the genome, of which 13 regions remained significantly associated with reduced fertility after rigorous cross-validation; these hotspots contained 17 candidate genes previously implicated in oocyte and embryonic development. These findings provide breeders and genetic counsellors with actionable genomic markers to identify and mitigate inbreeding depression affecting mare fertility, whilst advancing our understanding of the biological mechanisms linking homozygosity to reproductive outcomes in horses. The chromosome-level variability observed suggests that not all regions of inbreeding carry equal reproductive risk, offering scope for more refined selective breeding strategies that preserve desirable traits whilst protecting fertility.
Read the full abstract on PubMed
Practical Takeaways
- •Breeding decisions in Pura Raza Española and similar closed populations should prioritize reducing homozygosity and inbreeding coefficients to maintain mare fertility
- •Genomic testing for runs of homozygosity could help identify at-risk mares before fertility problems emerge, enabling early intervention or breeding plan adjustments
- •Genetic diversity management is critical in performance horse breeding programs to prevent inbreeding depression and associated subfertility
Key Findings
- •Negative correlation between whole-genome homozygosity and fertility (ρ = -0.144), strengthening to -0.241 in the 10% most/least fertile individuals
- •Identified 13 genomic regions (ROHi) significantly associated with fertility after cross-validation, containing 17 candidate genes related to oocyte and embryo development
- •Least fertile mares showed approximately 30% increase in average inbreeding values compared to most fertile mares
- •Chromosome-level analysis revealed wide variability in homozygosity-fertility correlation across the genome