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Genes2025; 16(2); 131; doi: 10.3390/genes16020131

Comparative Analysis of Genomic and Pedigree-Based Approaches for Genetic Evaluation of Morphological Traits in Pura Raza Española Horses.

Abstract: The single-step best linear unbiased predictor (ssGBLUP) has emerged as a reference method for genomic selection in recent years due to its advantages over traditional approaches. Although its application in horses remains limited, ssGBLUP has demonstrated the potential to improve the reliability of estimated breeding values in livestock species. This study aimed to assess the impact of incorporating genomic data using single-step restricted maximum likelihood (ssGREML) on reliability (R) in the Pura Raza Española (PRE) horse breed, compared to traditional pedigree-based REML. Methods: The analysis involved 14 morphological traits from 7152 animals, including 2916 genotyped individuals. Genetic parameters were estimated using a multivariate model. Results: Results showed that heritability estimates were similar between the two approaches, ranging from 0.08 to 0.76. However, a significant increase in reliability (R) was observed for ssGREML compared to REML across all morphological traits, with overall gains ranging from 1.56% to 13.30% depending on the trait evaluated. R ranged from 6.93% to 22.70% in genotyped animals, significantly lower in non-genotyped animals (0.82% to 12.37%). Interestingly, individuals with low R values in REML demonstrated the largest R gains in ssGREML. Additionally, this improvement was much greater (5.96% to 19.25%) when only considering stallions with less than 40 controlled foals. Conclusions: Hereby, we demonstrated that the application of genomic selection can contribute to improving the reliability of mating decisions in a large horse breeding program such as the PRE breed.
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Publication Date: 2025-01-23 PubMed ID: 40004460PubMed Central: PMC11855142DOI: 10.3390/genes16020131Google Scholar: Lookup
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  • Journal Article
  • Comparative Study

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.

The article discusses a study aimed to compare the efficiency of the single-step best linear unbiased predictor (ssGBLUP), a genomic approach, and traditional pedigree-based restricted maximum likelihood (REML) in genetic evaluation of morphological traits in Pura Raza Española (PRE) horse breed. The study found that the ssGBLUP showed a significant increase in reliability for all morphological traits compared to REML.

Methodology

  • The study centered around the assessment of 14 morphological traits in 7152 Pura Raza Española (PRE) horses. It involved 2916 genotyped horses (animals whose genetic material has been analyzed).
  • Genetic parameters of the traits were estimated through a multivariate model, a mathematical model consisting of multiple variables.

Results

  • The study found little variation in heritability estimates between the two methods, with estimates ranging from 0.08 to 0.76.
  • The single-step genomic best linear unbiased predictor (ssGBLUP) method showed a significant increase in reliability over the traditional pedigree-based restricted maximum likelihood (REML) method. The overall gains ranged from 1.56% to 13.30% depending on the specific trait being evaluated.
  • For the genotyped animals, the reliability ranged between 6.93% and 22.70%. This was substantially higher than the reliability range for non-genotyped animals, which stood at 0.82% to 12.37%.
  • The study observed the largest reliability gains in individuals with low reliability values under the REML method when evaluated using the ssGBLUP. Additionally, this improvement was considerably greater (5.96% to 19.25%) when the focus lay on stallions with less than 40 controlled foals.

Conclusion

  • The research concluded that the use of genomic selection, particularly the ssGBLUP method, can significantly improve the reliability of mating decisions in large horse breeding programs, such as the PRE breed, thus optimizing the genetic evaluation process.

Cite This Article

APA
Ziadi C, Demyda-Peyrás S, Valera M, Perdomo-González D, Laseca N, Rodríguez-Sainz de Los Terreros A, Encina A, Azor P, Molina A. (2025). Comparative Analysis of Genomic and Pedigree-Based Approaches for Genetic Evaluation of Morphological Traits in Pura Raza Española Horses. Genes (Basel), 16(2), 131. https://doi.org/10.3390/genes16020131

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 16
Issue: 2
PII: 131

Researcher Affiliations

Ziadi, Chiraz
  • Departamento de Genética, Universidad de Córdoba, 14014 Córdoba, Spain.
Demyda-Peyrás, Sebastián
  • Departamento de Genética, Universidad de Córdoba, 14014 Córdoba, Spain.
Valera, Mercedes
  • Departamento de Agronomía, ETSIA, Universidad de Sevilla, 41013 Sevilla, Spain.
Perdomo-González, Davinia
  • Departamento de Producción Animal, Universidad Complutense de Madrid, 28040 Madrid, Spain.
Laseca, Nora
  • Departamento de Agronomía, ETSIA, Universidad de Sevilla, 41013 Sevilla, Spain.
  • Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41014 Sevilla, Spain.
Rodríguez-Sainz de Los Terreros, Arancha
  • Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41014 Sevilla, Spain.
Encina, Ana
  • Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41014 Sevilla, Spain.
Azor, Pedro
  • Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41014 Sevilla, Spain.
Molina, Antonio
  • Departamento de Genética, Universidad de Córdoba, 14014 Córdoba, Spain.

MeSH Terms

  • Animals
  • Horses / genetics
  • Pedigree
  • Breeding
  • Genomics / methods
  • Phenotype
  • Genotype
  • Male
  • Quantitative Trait, Heritable
  • Female

Grant Funding

  • Equigenom GO / Ministry of Agriculture, Fisheries and Food, through the Spanish Agrarian Guarantee Fund, FEGA
  • RyC2022 Fellow / MINECO, Spain

Conflict of Interest Statement

The authors declare no conflicts of interest.

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Citations

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  4. Ziadi C, Valera M, Laseca N, Perdomo-González D, Demyda-Peyrás S, de Los Terreros AR, Molina A. Enhanced Reliability of the Evaluation of Fertility Traits in Pura Raza Española Horses Using Single-Step Genomic Best Linear Unbiased Prediction. Genes (Basel) 2025 May 9;16(5).
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