Genetic inbreeding depression load for conformation defects and dressage traits in the Pura Raza Española horse.

Objective Overview

• This study examined how genetic inbreeding affects specific dressage performance traits and conformational defects in the Pura Raza Española (PRE) horse breed.
• It quantified the inbreeding depression load to understand trait deterioration linked to inbreeding and evaluated how this information could improve breeding decisions.

Introduction to the Study

• The research focused on the genetic consequences of inbreeding within the PRE horse population, a well-known breed valued for dressage.
• Inbreeding depression refers to reduced performance or health due to increased homozygosity of deleterious alleles from related breeding.
• The traits analyzed included two dressage performance parameters—Walk and Points per Reprise (PPR)—and two conformational defects—Closed hocks and Convergent hocks.
• The aim was to quantify the genetic inbreeding depression load (IDL) and understand its impact on these traits.

Data and Methods

• Data comprised:
  • 43,838 records for performance traits (Walk and PPR)
  • 57,949 records related to hock conformation defects (Closed and Convergent hocks)
  • Pedigree information covering over 400,000 horses, enabling deep inbreeding coefficient calculations
• Inbreeding coefficients calculated:
  • F: Traditional individual inbreeding coefficient
  • F6: Recent inbreeding coefficient accounting for the last 6 generations
  • Fk: Other specific inbreeding metrics
  • Fij: Partial individual inbreeding coefficients showing the contribution of specific ancestors
• Statistical models used:
  • Bayesian methods to estimate the relationship between inbreeding and trait expressions
  • Linear regression for continuous traits like Walk and PPR
  • Ordinal logistic regression for categorical defect traits
  • Pearson correlation to study relationships between IDL across different traits

Key Results

• Inbreeding depression was significant for both dressage traits (Walk and PPR), meaning increased inbreeding negatively affected performance.
• The effect was strongest for more recent inbreeding (F6), highlighting that recent relatedness has a higher impact than older inbreeding.
• For conformation defects:
  • Closed hocks showed a clear positive association with higher inbreeding, indicating increased defect prevalence with inbreeding.
  • Convergent hocks showed mixed results, suggesting the relationship with inbreeding may be more complex or trait-specific.
• Heritability findings:
  • Low heritability for gait traits (~0.02), meaning most variation is not explained by genetics alone.
  • Moderate heritability for conformational defects (0.15-0.22), indicating some genetic control over these defects.
• Only a small fraction of animals had favorable IDL values at 10% inbreeding:
  • 2.94% for Walk
  • 0.77% for PPR
  • 1.30% for Closed hock
  • 0.69% for Convergent hock
• The distinction made between heritability and IDL:
  • Heritability reflects observable genetic variation currently expressed in the population.
  • IDL ratios show the potential variation due to inbreeding depression, regardless of whether it’s currently visible.
• Correlation analysis:
  • Moderate positive correlation between IDL for Walk and PPR traits (0.45), indicating related inbreeding effects on these performance traits.
  • Lower correlations between gait traits and defect traits suggest that genetic inbreeding affects these types of traits differently.

Implications and Conclusions

• Modeling individual-specific IDL is important for more accurate genetic evaluations in PRE horses.
• IDL explains a significant portion of phenotypic variation, highlighting that ignoring inbreeding depression could overlook critical aspects of genetic health and performance.
• Different traits exhibit distinct patterns of inbreeding depression, emphasizing the need for trait-specific strategies in breeding programs.
• Incorporating IDL into selection decisions allows breeders to:
  • Retain valuable genetic lines without excessive inbreeding
  • Reduce the expression of detrimental traits associated with inbreeding
  • Make breeding more sustainable by managing genetic diversity and animal health simultaneously