Pedigree-Based Assessment of Inbreeding Effects on Conformation and Performance Traits in the Peruvian Paso Horse: Implications for Sustainable Genetic Improvement

Objective: The aim of this study was to analyze inbreeding depression in the Peruvian paso horse (PPH), with a focus on its effects on morphometric, physiological, and functional traits. Methods: A total of 35 traits were evaluated in 148 animals, using pedigree records up to 2023 provided by the National Association of Breeders and Owners of the PPH. Multivariate animal models were employed to estimate heritability, and a Best Linear Unbiased Prediction (BLUP) model was applied to calculate estimated breeding values (EBVs), accounting for fixed effects including sex, stud farm, gait speed, and age. Results: The findings indicate that both the inbreeding coefficient (F) and its rate of change (ΔF) have significant effects on multiple traits. Pedigree analyses revealed that both parents recorded for over 94% of animals, indicating good pedigree depth. Certain historical periods were identified as having reduced ancestral diversity, highlighting the importance of monitoring genetic diversity to prevent population bottlenecks. The number of equivalent complete generations ranged from 2.355 to 8.417 between 1970 and 2023. Inbreeding exerted a negative impact on key traits such as withers height and scapulo-humeral angle. Furthermore, ΔF demonstrated a more immediate and pronounced effect on specific traits. Notably, differential impacts were observed between F and ΔF. Correlations between EBVs calculated with and without inclusion of inbreeding as a covariate were significantly below 0.99 for certain traits, suggesting that inbreeding introduces estimation bias, likely due to the expression of recessive deleterious alleles. Conclusions: Our results demonstrate that inbreeding affects not only linear body measurements but also anatomical angles, potentially reflecting the influence of pleiotropic genes affecting multiple morphological traits. Moreover, functional and physiological traits were found to be particularly sensitive to inbreeding effects, underscoring the need for strategic genetic management in this breed.