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Genetics, selection, evolution : GSE2026; 58(1); 59; doi: 10.1186/s12711-026-01075-4

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. Results: 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. Conclusions: 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.
© 2026. The Author(s).
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Publication Date: 2026-08-05 PubMed ID: 42638080PubMed Central: 1210738DOI: 10.1186/s12711-026-01075-4Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study investigated the role of dominance genetic effects in reproductive and morphological traits of Pura Raza Española (PRE) mares to understand their implications for breeding value estimation and mating strategies.
  • The research highlights how incorporating dominance deviations can affect genetic management and potentially enhance the phenotypic performance of offspring in this horse breed.

Background and Rationale

  • Dominance Effects: These refer to non-additive genetic interactions between alleles at the same locus which influence traits but are often overlooked in breeding programs due to estimation difficulties.
  • Challenges in Animal Breeding: Traditional approaches mostly focus on additive genetic variance, ignoring dominance due to complex computations and low accuracy when using pedigree data.
  • Importance of the Study: Determining whether dominance variance is significant enough to affect breeding decisions, such as mating designs or breeding value predictions, especially in a popular horse breed like the PRE.

Traits Analyzed

  • Reproductive Traits:
    • Age at First Foaling (AFF)
    • Reproductive Efficiency (RE)
    • Interval Between First and Second Foaling (I12)
  • Morphological Traits:
    • Scapulo-Ischial Length (SIL)
    • Dorsal Sternal Diameter (DSD)
    • Knee Circumference (KC)

Data and Methodology

  • Population: 3,967 PRE mares with available reproductive and morphological records; the pedigree included 11,331 individuals with an average relatedness of 5%.
  • Data Selection:
    • Mares with full sisters and at least one foaling were specifically chosen to improve the accuracy of genetic parameter estimates.
    • Additional records from other females foaling in the same stud and year were included for robustness.
  • Pedigree Analysis:
    • Condensed probabilities of identity by descent were calculated using a recursive algorithm to estimate relatedness and inbreeding effects.
  • Statistical Modeling:
    • A linear mixed model was used to estimate variance components, including dominance variance, additive variance, and their covariance.
    • Dominance variance was decomposed into components for relationships among non-inbred and inbred individuals, considering correlations with additive effects.

Key Results

  • Heritability Estimates:
    • Broad-sense heritability (total genetic variance including additive and dominance effects) ranged from 0.20 (for RE) to 0.64 (for SIL), indicating notable genetic control especially for morphological traits.
    • Narrow-sense heritability (additive genetic variance only) ranged between 0.05 (I12) and 0.39 (KC), suggesting that additive effects alone may underestimate trait heritability in some cases.
  • Additive-Dominance Correlations:
    • Negative correlations detected, ranging from -0.43 (RE and I12) to -0.69 (DSD), which implies an inverse relationship between additive and dominance effects for certain traits.
  • Dominance Effects on Phenotypes:
    • Incorporating dominance deviations into mating design showed potential phenotypic performance improvements in newborn foals, ranging from a modest 0.05% increase (DSD) to a meaningful 3.4% increase (I12).

Conclusions and Implications

  • Relevance of Dominance in PRE Horses: Dominance deviations are significant and should not be ignored as they impact the estimation of genetic parameters and may bias expected selection responses if unaccounted for.
  • Genetic Management Recommendations:
    • Breeding programs that incorporate dominance variance can improve estimation accuracy of breeding values.
    • Mating strategies that consider dominance deviations can maximize overall genetic and phenotypic performance of offspring.
    • Ignoring dominance could lead to suboptimal decisions in selection and mating.
  • Future Directions: Implementation of breeding models that include dominance effects could provide enhanced genetic gain and better management of PRE horse populations.

Cite This Article

APA
Perdomo-González DI, Valera M, Molina A, Azor P, Sánchez JP. (2026). Implications of dominance deviations for reproductive and morphological traits in the genetic management of the Pura Raza Española horse. Genet Sel Evol, 58(1), 59. https://doi.org/10.1186/s12711-026-01075-4

Publication

Genetics, selection, evolution : GSE
ISSN: 1297-9686
NlmUniqueID: 9114088
Country: France
Language: English
Volume: 58
Issue: 1
PII: 59

Researcher Affiliations

Perdomo-González, Davinia I
  • Dpto. de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain. daperdom@ucm.es.
Valera, Mercedes
  • Dpto. Agronomía, ETSIA, Universidad de Sevilla, Ctra. Utrera Km, 41005, Seville, Spain.
Molina, Antonio
  • Dpto. Genética, Universidad de Córdoba, Ctra. Madrid-Córdoba Km 396, 14071, Córdoba, Spain.
Azor, Pedro
  • Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41012, Seville, Spain.
Sánchez, Juan P
  • Dpto. Genética, Universidad de Córdoba, Ctra. Madrid-Córdoba Km 396, 14071, Córdoba, Spain.

MeSH Terms

  • Animals
  • Female
  • Horses / genetics
  • Horses / anatomy & histology
  • Horses / physiology
  • Pedigree
  • Reproduction / genetics
  • Genes, Dominant
  • Breeding
  • Phenotype
  • Models, Genetic
  • Quantitative Trait, Heritable

Grant Funding

  • PRJ202304988 / Ministerio de Ciencia e Innovación

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests.

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