Implications of dominance deviations for reproductive and morphological traits in the genetic management of the Pura Raza Española horse

Abstract

Dominance is a non-additive genetic effect involving allele interaction at the same locus. In animal breeding, it has often been ignored due to its complexity and the low accuracy of pedigree-based estimates. This study analysed dominance variance components for reproductive traits [age at first foaling (AFF), reproductive efficiency (RE), interval between first and second foaling (I12)] and morphological traits [scapulo-ischial length (SIL), dorsal sternal diameter (DSD), knee circumference (KC)] in Pura Raza Española (PRE) mares. The aim was to assess the magnitude of dominance effects across traits to determine whether alternative models are required for breeding value estimation or if dominance deviation predictions should be reconsidered in strategies such as mating design. Mares with full sisters and at least one foaling were identified and additional records of other females foaling in the same stud and year were also selected. The number of mares with reproductive and morphologic records was 3967 and the pedigree included 11,331 individuals with an average relatedness coefficient of 5%. First, condensed probabilities of identity based on pedigree data were estimated using a recursive algorithm. Next, a linear model in which variance components (dominance, additive and their covariance) were estimated, using the pedigree and phenotypic data. The dominance variance was partitioned into a term linked to relationships between non-inbred individuals and another linked to relationships between inbred individuals, with the latter assumed to be correlated with the additive effect. The broad-sense heritability values oscillated between 0.64 (SIL) and 0.20 (RE) while the narrow-sense heritability ranged between 0.05 (I12) and 0.39 (KC) and estimates of the additive-dominance correlation varied between − 0.43 (RE and I12) and − 0.69 (DSD). The consideration of dominance deviations in mating design would allow a relative increase of 0.05% (DSD) to 3.4% (I12) in the phenotypic performances of newborns foals. Dominance deviations represent a relevant genetic phenomenon in the PRE breeding programme. If ignored, they may bias additive variance estimates and lead to an overestimation of expected selection response. Models that include dominance effects could be valuable for designing mating strategies aimed at maximising the overall genetic value and phenotypic performance of newborn foals.