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

Abstract

Objective: Investigate the genetic inbreeding depression load (IDL) on two dressage traits and two conformational defects in horses. Methods: The dataset included performance records for Walk and Points per Reprise (PPR) (N:43,838) and conformation data for Closed and Convergent hocks (N:57,949). Pedigree information spanned over 400,000 individuals. Inbreeding coefficients (F, F6, Fk) and partial inbreeding coefficient (Fij) were computed to quantify the IDL using Bayesian approach. Linear and ordinal logistic regressions were used to assess the relationship between inbreeding and phenotypic values. Additionally, Pearson correlations were computed to explore IDL relationships across traits. Results: Significant inbreeding depression was detected for Walk and PPR across all inbreeding coefficients, with stronger effects for recent inbreeding (F6). Closed hock showed significant positive associations with inbreeding, while Convergent hock displayed mixed responses. Heritability estimates were low for gait traits (0.02) and moderate for defects (0.15-0.22). Only a small percentage of animals exhibited favorable IDL values for a 10% inbreeding: 2.94% (Walk), 0.77% (PPR), 1.30% (Closed hock), and 0.69% (Convergent hock). While heritability reflects the variation actually observed within a population, IDL ratios indicate the possible variation that exists, regardless of whether it is currently expressed or not. Pearson correlations revealed moderate positive IDL associations between Walk and PPR (0.45), and lower correlations between gait and defect traits. Conclusion: Results highlight the importance of modeling individual-specific IDL in Pura Raza Española genetic evaluations. IDL explained a substantial proportion of phenotypic variance and showed trait-specific patterns. Incorporating IDL into selection strategies enables more informed breeding decisions, allowing the retention of valuable genetic lines while minimizing deleterious inbreeding effects, thereby supporting more sustainable and resilient genetic improvement.