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

Background: Inbreeding is caused by mating between related individuals and is associated with reduced ftness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associ‑ ated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological traits and two morphology defects in the Pura Raza Española (PRE) horse breed. Results: The regression coefcients that were calculated between trait performances and inbreeding coefcients demonstrated the existence of inbreeding depression. In total, 58,772,533 partial inbreeding coefcients (Fij) were esti‑ mated for the whole PRE population (328,706 horses). We selected the descendants of horses with a Fij≥6.25% that contributed to at least four ofspring and for which morphological traits were measured for the subsequent analysis of inbreeding depression load (639 horses). A pedigree was generated with the last fve generations (5026 animals) used as the reference population (average inbreeding coefcient of 8.39% and average relatedness coefcient of 10.76%). Heritability estimates ranged from 0.08 (cresty neck) to 0.80 (height at withers), whereas inbreeding depression load ratios ranged from 0.01 (knock knee) to 0.40 (length of shoulder), for an inbreeding coefcient of 10%. Most of the correlations between additive and inbreeding depression load genetic values and correlations between inbreeding depression load genetic values for the diferent traits were positive or near 0. Conclusions: Although the average inbreeding depression loads presented negative values, a certain percentage of the animals showed neutral or even positive values. Thus, high levels of inbreed