Genome-wide association study reveals candidate loci on ECA1 and ECA9 for withers height in Friesian horses.
Abstract: In Friesian horses, withers height is an important trait as a minimum has been set to be eligible to the studbook. Several loci for withers height have been identified in horses. However, withers height has not been studied in the Friesian horse. Therefore, our aim was to identify loci associated with withers height in the Friesian horse population. We performed a genome-wide association study using 70 K SNP data of 2192 Friesian horses. We found ECA1 and ECA9 to be significantly associated with withers height, explaining 19.6% and 3.5% of the phenotypic variance, respectively. In other horse breeds, the LCORL/NCPAG locus on ECA3 showed the strongest association with withers height, but here we found that the best-associated SNP for that locus is nearly fixed in Friesian horses for the allele associated with small size. Moreover, we observed a clear decline followed by a marked increase in average withers height of the Friesian horse over time, probably owing to shifts in its primary use over the course of the years. Additionally, the frequency of the best-associated SNP on ECA1 has increased over time. Together, our study showed that ECA1 and ECA9 are associated with withers height in Friesian horses. Further studies should be performed to confirm candidate causal mutations.
© 2025 The Author(s). Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.
Publication Date: 2025-10-15 PubMed ID: 41090464PubMed Central: PMC12522178DOI: 10.1111/age.70049Google Scholar: Lookup
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- Journal Article
Summary
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Overview
- This study investigated the genetic factors influencing withers height, a key trait for Friesian horses’ studbook eligibility.
- Using genome-wide association study (GWAS) techniques, the research identified significant genetic loci on chromosomes ECA1 and ECA9 linked to withers height in Friesian horses.
Background and Importance
- Withers height is a critical trait in horses, especially for Friesian horses, where a minimum height criterion determines studbook admission.
- Previous research in various horse breeds has pinpointed several genetic loci affecting withers height.
- However, the genetic basis for withers height specifically in Friesian horses had not been previously explored.
Research Objective
- To identify genetic loci associated with withers height in the Friesian horse breed.
Methodology
- A genome-wide association study (GWAS) was conducted using SNP array data covering 70,000 single nucleotide polymorphisms (SNPs).
- The sample consisted of 2,192 Friesian horses, providing robust statistical power.
- Statistical analyses searched for SNPs significantly linked to withers height variations.
Key Findings
- Two loci, located on chromosomes ECA1 and ECA9, were found significantly associated with withers height:
- The locus on ECA1 explained approximately 19.6% of the phenotypic variance in height.
- The locus on ECA9 explained about 3.5% of the variance.
- Contrary to findings in other breeds where the LCORL/NCPAG locus on chromosome ECA3 is typically most influential, the associated SNP for this locus is nearly fixed in Friesians for the allele linked to smaller size, indicating limited variation in this population at that locus.
- The study observed temporal trends in average withers height: a decline followed by a marked increase over time.
- This trend likely reflects changes in the breed’s primary use through the years, potentially affecting selection pressures.
- The frequency of the SNP on ECA1 associated with withers height increased over time, indicating possible selective breeding favoring this allele.
Significance and Implications
- Identification of ECA1 and ECA9 loci provides new candidate genetic regions influencing height in Friesian horses, which differ from loci identified in other horse breeds.
- The nearly fixed allele at ECA3 suggests breed-specific genetic architecture governing withers height.
- Temporal changes in allele frequencies and phenotypes highlight the influence of breeding practices and selection on genetic traits.
- The findings could help breeders make more informed decisions to optimize height traits in Friesian horses, maintaining studbook standards.
Recommendations for Future Research
- Further studies should focus on pinpointing the exact causal mutations within the candidate loci on ECA1 and ECA9.
- Functional analyses could clarify the biological mechanisms by which these genetic regions influence withers height.
- Longitudinal studies could better elucidate how selective breeding impacts the genetic architecture over generations.
Cite This Article
APA
Steensma MJ, Doekes HP, Derks MFL, Ducro BJ.
(2025).
Genome-wide association study reveals candidate loci on ECA1 and ECA9 for withers height in Friesian horses.
Anim Genet, 56(5), e70049.
https://doi.org/10.1111/age.70049 Publication
Researcher Affiliations
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
- Koninklijke Vereniging 'het Friesch Paarden-Stamboek', Drachten, DP, The Netherlands.
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
MeSH Terms
- Animals
- Horses / genetics
- Polymorphism, Single Nucleotide
- Genome-Wide Association Study / veterinary
- Phenotype
- Breeding
Grant Funding
- 4164023400 / Topconsortium voor Kennis en Innovatie
Conflict of Interest Statement
The authors declare that they have no competing interests.
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