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Home / Equine Research Bank / J Anim Breed Genet / Single-Step Genome-Wide Association Study of Factors for Eva...
Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie2025; 142(5); 499-512; doi: 10.1111/jbg.12923

Single-Step Genome-Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses.

Abstract: Swedish Warmblood horses (SWB) are bred for show jumping and/or dressage with young horse test scores as indicator traits. This study aimed to investigate possible candidate genes and regions of importance for evaluated and linearly scored young horse test traits. A single-step genome-wide association study (ssGWAS) was done using the BLUPF90 suite of programs for factors scores from factor analysis of traits assessed at young horse tests together with height at withers. The ssGWAS included 20,814 SWB with factors scores for four factors for evaluated traits. A total of 6436 of these horses also had factor scores for 13 factors for linearly scored traits. Genotypes from a 670K SNP array were available for 380 of the horses in this study. All genotyped horses had factor scores for evaluated traits, and 379 also had factors scores for linearly scored traits. Significant SNPs associated with three factors related to size were located on ECA3 within or nearby a well-known region, including the genes ligand dependent nuclear receptor corepressor like (LCORL), non-SMC condensin I complex subunit G (NCAPG), DDB1 and CUL4 Associated Factor 16 (DCAF16), and the Family with Sequence Similarity 184 Member B (FAM184B). Significant SNPs were also detected for two factors for evaluated traits representing conformation and jumping, and four factors for linearly scored traits related to body length, neck conformation, walk and trot (hindleg position and activity), respectively. Among nearby genes, calcium/calmodulin-dependent protein kinase type 1D (CAMK1D) for the factor for linearly scored traits related to neck conformation and GLI Family Zinc Finger 2 (GLI2) for the factor for evaluated jumping traits, were most promising. For these, top associated SNPs were detected within the genes, and the known gene functions seems to be related to the phenotypes. In conclusion, ssGWAS is beneficial to detect plausible candidate genes/regions for desired traits in warmblood horses.
© 2025 The Author(s). Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.
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Publication Date: 2025-01-04 PubMed ID: 39754479PubMed Central: PMC12340361DOI: 10.1111/jbg.12923Google Scholar: Lookup
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  • Journal Article

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.

This study investigates potential genes and regions significant for certain traits in Swedish Warmblood Horses, using a single-step genome-wide association study. It reveals genes potentially linked to horse size, conformation, jumping ability, and gaits such as trotting and walking.

Objective and Methodology

  • The research aims to identify potential genes and regions within the genome that may influence young horse test traits in Swedish Warmblood horses, which are bred specifically for dressage and show jumping.
  • To achieve this aim, a single-step genome-wide association study (ssGWAS) was employed.
  • This method allows the researchers to simultaneously analyze the data of both genotyped and non-genotyped horses, enhancing the robustness of the results.
  • Factor scores from factor analysis of traits were evaluated at young horse tests, generating information on four different factors for ‘evaluated’ traits.
  • Genotype data from a 670K SNP array was available for a select group of horses within the study. These horses also had factor scores for ‘evaluated’ traits, providing a correlation worth investigating.

Results: Significant Associations

  • Several SNPs (single nucleotide polymorphisms) within specific genes were found to be significantly associated with different evaluated traits.
  • Three factors were related to the size of the horse, all of which were located within a region of equine chromosome 3 (ECA3) that includes several well-studied genes.
  • The genes in this region are ligand dependent nuclear receptor corepressor like (LCORL), non-SMC condensin I complex subunit G (NCAPG), DDB1 and CUL4 Associated Factor 16 (DCAF16), and the Family with Sequence Similarity 184 Member B (FAM184B).
  • Various significant SNPs for two factors related to traits of conformation and jumping, and four factors related to linearly scored traits of body length, neck conformation, walk, and trot (hindleg position and activity) were identified.
  • The calcium/calmodulin-dependent protein kinase type 1D (CAMK1D) gene and the GLI Family Zinc Finger 2 (GLI2) gene were the most promising nearby genes. These genes are linked to neck conformation and evaluated jumping traits, respectively.

Conclusion

  • The study concludes that the ssGWAS methodology can successfully reveal potential candidate genes and regions that might be relevant for the selective breeding of specific traits in Swedish Warmblood horses.
  • This can have benefits not just for Swedish Warmblood horses, but broadly for warmblood horses, enhancing opportunities for selective breeding based on desirable characteristics.
  • The results also open up potential for further research into gene behavior in equine species and additional studies into the role of the identified genes in shaping these traits.

Cite This Article

APA
Nazari-Ghadikolaei A, Fikse WF, Viklund ÅG, Mikko S, Eriksson S. (2025). Single-Step Genome-Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses. J Anim Breed Genet, 142(5), 499-512. https://doi.org/10.1111/jbg.12923

Publication

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
ISSN: 1439-0388
NlmUniqueID: 100955807
Country: Germany
Language: English
Volume: 142
Issue: 5
Pages: 499-512

Researcher Affiliations

Nazari-Ghadikolaei, Anahit
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Fikse, W Freddy
  • Växa, Uppsala, Sweden.
Viklund, Åsa Gelinder
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Mikko, Sofia
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Eriksson, Susanne
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.

MeSH Terms

  • Animals
  • Horses / genetics
  • Genome-Wide Association Study
  • Polymorphism, Single Nucleotide
  • Phenotype
  • Genotype
  • Sweden
  • Male
  • Female

Grant Funding

  • H1147215 / The Swedish-Norwegian Foundation for Equine Research

Conflict of Interest Statement

The Swedish Warmblood Association has provided the phenotype and pedigree data for this study, and Åsa Gelinder Viklund has regular commitments to Swedish Warmblood Association, regarding the routine genetic evaluation. We declare that there are no other conflicts of interest.

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