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Limb-conformation defects significantly influence equine performance and welfare, necessitating thorough investigation for effective management. This study examines the prevalence and genetic parameters of 14 limb-conformation defects in Menorca Purebred horses using data from 1120 records (509 animals with an average age of 101.87 ± 1.74 months) collected between 2015 and 2023. Defects were evaluated using a three-class scale by three appraisers, and a Bayesian approach via Gibbs sampling was employed to estimate genetic parameters including gender, birth period, stud selection criteria, evaluation age and appraiser as fixed effects. Splay-footed forelimb and closed hocks were the most prevalent defects (67.20% and 62.53%, respectively). Horses with any of the defects analyzed have been observed to obtain significantly lower scores for both walk and trot. Heritability estimates range from 0.12 (s.d.: 0.025) for closed hock to 0.30 (s.d.: 0.054) for base narrow, confirming the genetic influences on the expression of limb conformation defects. The divergent defect in hind limbs showed the highest genetic correlations with forelimb defects (camped under, −0.69; s.d: 0.32 and camped out, 0.70; s.d: 0.27). The significant genetic correlations between defects highlight the complexity of the relationships, which requires careful consideration.

Abstract Background Inbreeding is caused by mating between related individuals and is associated with reduced fitness 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 associated 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 coefficients that were calculated between trait performances and inbreeding coefficients demonstrated the existence of inbreeding depression. In total, 58,772,533 partial inbreeding coefficients (F ij) were estimated for the whole PRE population (328,706 horses). We selected the descendants of horses with a F ij ≥ 6.25% that contributed to at least four offspring and for which morphological traits were measured for the subsequent analysis of inbreeding depression load (639 horses). A pedigree was generated with the last five generations (5026 animals) used as the reference population (average inbreeding coefficient of 8.39% and average relatedness coefficient 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 coefficient of 10%. Most of the correlations between additive and inbreeding depression load genetic values and correlations between inbreeding depression load genetic values for the different 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 inbreeding do not always lead to a decrease in mean phenotypic value or an increase in morphological defects. Hence, individual inbreeding depression loads could be used as a tool to select the most appropriate breeding animals. The possibility of selecting horses that have a high genetic value and are more resistant to the deleterious effects of inbreeding should help improve selection outcomes.

The studbook of Pura Raza Menorquina horses only permits the use of black-coated animals with a small quantity of white marks as breeding stock. Its breeding program uses linear morpho-functional traits as selection criteria. Our aim was to estimate the genetic parameters of linear morpho-functional traits, and reveal relationship of quality of black coat color (QB) and percentage of white marks (WM) with the other morphological and functional linear traits in this breed. A total of 46 linear traits were scored by four appraisers using seven classes, with a total of 772 records from 333 animals (≥4 years old). Univariate animal models using a Bayesian approach were used, with a pedigree of 757 animals. Sex (two) and appraiser-season (13) were included as fixed effects, age as a linear covariate, and permanent environmental and additive genetic as random effect. The heritabilities of the morpho-functional traits were low to medium (0.09–0.58) and matched the range in the bibliography. Heritabilities for coat color traits were 0.36 for QB and 0.23 for WM. The highest genetic correlations were obtained between QB and upper neck line (0.816) and between WM and form of the hoof (0.638). The negative signs of most of the genetic correlations between WM and the functional traits is also remarkable, contributing to the selection of functional traits against the presence of white marks in this population. A clear genetic differentiation was observed between animals with better breeding values for QB and WM, corroborated by a study on founders. In conclusion, QB and WM could show different genetic backgrounds.

Horses have been valued for their diversity of coat color since prehistoric times. In particular, the pleiotropic effect that coat color genes have on behavior determines the way the horse perceives and reacts to its environment. The primary aim of this study was to evaluate the influence of coat color on basal reactivity assessed with infrared thermography as eye temperature at rest (ETR), determine their relation with the results obtained by these horses in Show Jumping competitions and to estimate the genetic parameters for this variable to test its suitability for genetic selection. A General Linear Model (GLM) and Duncan post-hoc analysis indicated differences in ETR due to coat color, sex, age, location, and breed-group factors. A Spearman’s rank correlation of 0.11 (p < 0.05) was found with ranking, indicating that less reactive horses were more likely to achieve better rankings. Heritability values ranged from 0.17 to 0.22 and were computed with a model with genetic groups and a model with residual variance heterogeneity. Breeding values were higher with the last genetic model, thus demonstrating the pleiotropic effect of coat color. These results indicate that ETR has a suitable genetic basis to be used in the breeding program to select for basal reactivity due to coat color.

Ewe Neck is a relatively common morphological defect in Pura Raza Español (PRE) horses and other Baroque type horse breeds, which adversely affects the breeding industry; (1) objectives: to establish the within-breed prevalence, possible associated factors, and heritability of Ewe Neck in PRE horses; (2) methods: the database included evaluations of 35,267 PRE horses. The Ewe Neck defect, 16 morphological traits, and 4 body indices were recorded. A Bayesian genetic animal model included the following systematic effects: sex, age, coat color, geographical area of the stud, and birth stud size were used; (3) results: in this PRE population, a total of 27.12% was affected. All the risk factors studied were significantly associated with the Ewe Neck score. The heritability coefficient for Ewe Neck score ranged from 0.23 to 0.34. Morphological traits (height at chest, length of back, head-neck junction, and bottom neck-body junction) and the indices (head and thoracic index) were those most closely related with the appearance of Ewe Neck; (4) conclusions: Ewe Neck is a relatively frequent defect in PRE horses, associated with risk factors and other morphological traits, with a moderate level of heritability. Breeding to select against this condition may therefore be beneficial in this breed.

The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the Fij with an average of 5370 descendants, with each descendant having an average of 170 CAs. Over the generations, the number of CAs has increased, while the proportion of Fij by each one has decreased. In addition, the contributions of the more influential ancestors have changed. The increased census, the limited use of artificial insemination and our increased knowledge about inbreeding depression and the animals’ breeding values allow breeders to select horses more for their functionality and conformation than for their pedigree reputation, which is the cause of all these changes.