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Home / Equine Research Bank / Animal / A genome-wide association study of mare fertility in the Pur...
Animal : an international journal of animal bioscience2022; 16(3); 100476; doi: 10.1016/j.animal.2022.100476

A genome-wide association study of mare fertility in the Pura Raza Español horse.

Abstract: Despite the economic importance of fertility for the horse industry, few efforts have been made to achieve a better understanding of the genetic mechanisms underlying its control. This is probably due to the difficulty of obtaining reliable phenotypes and the complexity of modelling the environmental and management factors. This work is novel in that we propose to use reproductive efficiency (RE) as an indicator of mare fertility. To achieve this, we performed a genome-wide association study in the Pura Raza Español horse aimed at identifying genomic variants, regions, and candidate genes associated with fertility in mares. The dataset included 819 animals genotyped with the Affymetrix Axiom™ Equine 670 K single-nucleotide polymorphisms (SNPs) Genotyping Array and the deregressed breeding values for RE trait, obtained using a ssBLUP model, employed as pseudo-phenotypic data. Our results showed 28 SNPs potentially associated with RE, which explained 87.19% of the genetic variance and 6.61% of the phenotypic variance. Those results were further validated in BayesB, showing a correlation between observed and predicted RE of 0.57. In addition, 15 candidate genes (HTRA3, SPIRE1, APOE, ERCC1, FOXA3, NECTIN-2, KLC3, RSPH6A, PDPK1, MEIOB, PAQR4, NM3, PKD1, PRSS21, IFT140) previously related to fertility in mammals were associated with the markers and genomic regions significantly associated with RE. To our knowledge, this is the first genome-wide association study performed on mare fertility.
Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.
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Publication Date: 2022-03-02 PubMed ID: 35247706DOI: 10.1016/j.animal.2022.100476Google Scholar: Lookup
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Summary

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This study investigates the genetic factors influencing fertility in the Pura Raza Español horse, identifying key genomic variants and genes. The research used a novel measure of reproductive efficiency (RE) as an indicator of fertility and validated the findings using the BayesB method.

Objective and Methodology

  • The research aims to understand the genetic aspects that control fertility in horses, specifically the Pura Raza Español breed.
  • Reproductive efficiency (RE), a new parameter, is proposed as an indicator of mare fertility.
  • A genome-wide association study was performed on 819 horses, which were genotyped using the Affymetrix Axiom™ Equine 670 K single-nucleotide polymorphisms (SNPs) Genotyping Array. Simultaneously, the deregressed breeding values for RE trait, calculated using a ssBLUP model, were used as pseudo-phenotypic data.

Results of the study

  • The study identified 28 single-nucleotide polymorphisms (SNPs) that are potentially associated with RE. These SNPs explained 87.19% of the genetic variance and 6.61% of the phenotypic variance.
  • The results were validated using BayesB, which showed a correlation of 0.57 between predicted and observed RE.
  • The analysis also identified 15 candidate genes (HTRA3, SPIRE1, APOE, ERCC1, FOXA3, NECTIN-2, KLC3, RSPH6A, PDPK1, MEIOB, PAQR4, NM3, PKD1, PRSS21, IFT140) that were previously linked to fertility in mammals.

Significance of the Study

  • This study contributes to a better understanding of the genetic factors affecting horse fertility. Such knowledge is crucial for the horse industry, especially for breeding programs.
  • This study is the first of its kind, being the first genome-wide association study performed on mare fertility. The novel use of RE as an indicator of fertility gives this study a unique approach.

Cite This Article

APA
Laseca N, Demyda-Peyrás S, Valera M, Ramón M, Escribano B, Perdomo-González DI, Molina A. (2022). A genome-wide association study of mare fertility in the Pura Raza Español horse. Animal, 16(3), 100476. https://doi.org/10.1016/j.animal.2022.100476

Publication

Animal : an international journal of animal bioscience
ISSN: 1751-732X
NlmUniqueID: 101303270
Country: England
Language: English
Volume: 16
Issue: 3
Pages: 100476
PII: S1751-7311(22)00023-4

Researcher Affiliations

Laseca, N
  • Departamento de Genética. Facultad de Veterinaria, Universidad de Córdoba, Campus de Rabanales, CN-IV km 396, 14071 Córdoba, España. Electronic address: ge2lagan@uco.es.
Demyda-Peyrás, S
  • Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 s/n, La Plata 1900, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) La Plata, La Plata 1900, Argentina.
Valera, M
  • Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica. Universidad de Sevilla, Ctra. Utrera, Km 1, Sevilla, Spain.
Ramón, M
  • Centro Regional de Selección y Reproducción Animal (CERSYRA), Av. del Vino, 10, 13300 Valdepeñas, Ciudad Real, Spain.
Escribano, B
  • Departamento de Fisiología, Universidad de Córdoba, Campus de Rabanales, CN-IV km 396, 14071 Córdoba, Spain.
Perdomo-González, D I
  • Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica. Universidad de Sevilla, Ctra. Utrera, Km 1, Sevilla, Spain.
Molina, A
  • Departamento de Genética. Facultad de Veterinaria, Universidad de Córdoba, Campus de Rabanales, CN-IV km 396, 14071 Córdoba, España.

MeSH Terms

  • Animals
  • Female
  • Fertility / genetics
  • Genome-Wide Association Study / veterinary
  • Genotype
  • Horses / genetics
  • Mammals / genetics
  • Phenotype
  • Polymorphism, Single Nucleotide

Citations

This article has been cited 10 times.
  1. Laseca N, Cánovas Á, Valera M, Id-Lahoucine S, Perdomo-González DI, Fonseca PAS, Demyda-Peyrás S, Molina A. Genomic screening of allelic and genotypic transmission ratio distortion in horse. PLoS One 2023;18(8):e0289066.
    doi: 10.1371/journal.pone.0289066pubmed: 37556504google scholar: lookup
  2. Dementieva N, Nikitkina E, Shcherbakov Y, Nikolaeva O, Mitrofanova O, Ryabova A, Atroshchenko M, Makhmutova O, Zaitsev A. The Genetic Diversity of Stallions of Different Breeds in Russia. Genes (Basel) 2023 Jul 24;14(7).
    doi: 10.3390/genes14071511pubmed: 37510415google scholar: lookup
  3. Jiménez JM, Morales RM, Menéndez-Buxadera A, Demyda-Peyrás S, Laseca N, Molina A. Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle. Animals (Basel) 2023 Jan 31;13(3).
    doi: 10.3390/ani13030501pubmed: 36766391google scholar: lookup
  4. Lin J, Xiang Y, Huang J, Zeng H, Zeng Y, Liu J, Wu T, Liang Q, Liang X, Li J, Zhou C. NAT10 Maintains OGA mRNA Stability Through ac4C Modification in Regulating Oocyte Maturation. Front Endocrinol (Lausanne) 2022;13:907286.
    doi: 10.3389/fendo.2022.907286pubmed: 35937804google scholar: lookup
  5. Ziadi C, Morales RM, Vargas-Pérez MÁ, Calvo-Rubio GA, Demyda-Peyrás S, Molina A. Multivariate Single-Step GWAS Reveals Pleiotropic Genomic Regions and Candidate Genes Associated with Male Scrotal Circumference and Female Fertility Traits in Retinta Beef Cattle. Vet Sci 2025 Oct 11;12(10).
    doi: 10.3390/vetsci12100977pubmed: 41150117google scholar: lookup
  6. Morales RM, Calvo-Rubio GA, Ziadi C, Vargas-Pérez MÁ, Demyda-Peyrás S, Molina A. Weighted Single-Step GWAS Reveals Genomic Regions Associated with Female Fertility in the Spanish Retinta Beef Cattle. Animals (Basel) 2025 Sep 11;15(18).
    doi: 10.3390/ani15182665pubmed: 41007908google scholar: lookup
  7. 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).
    doi: 10.3390/genes16050562pubmed: 40428384google scholar: lookup
  8. Sievers J, Distl O. Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse. Genes (Basel) 2025 Mar 11;16(3).
    doi: 10.3390/genes16030327pubmed: 40149478google scholar: lookup
  9. de Carvalho FE, Ferraz JBS, Pedrosa VB, Matos EC, Eler JP, Silva MR, Guimarães JD, Bussiman F, Silva BCA, Mulim HA, Rocha AO, Araujo AC, Wen H, Campos GS, Brito LF. Genetic parameters and genome-wide association studies including the X chromosome for various reproduction and semen quality traits in Nellore cattle. BMC Genomics 2025 Jan 10;26(1):26.
    doi: 10.1186/s12864-024-11193-2pubmed: 39794685google scholar: lookup
  10. De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024 Jan 23;14(1):2003.
    doi: 10.1038/s41598-023-48103-7pubmed: 38263320google scholar: lookup
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