Genetics of Swedish warmblood horses for conformation and jumping traits

Haplotype GWAS in swedish warmblood horses for conformation and jumping traits

J Anim Sci. 2026 Apr 10:skag109. doi: 10.1093/jas/skag109. Online ahead of print.
Authors
Michela Ablondi 1 2 , Susanne Eriksson 2 , Åsa Gelinder Viklund 2 , Sofia Mikko 2
Affiliations

1 Department of Veterinary Science, Università degli Studi di Parma, 43126, Italy Parma.
2 Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.

PMID: 41968096
DOI: 10.1093/jas/skag109

Abstract

The aim of this study was to better understand the genomic architecture behind performance-related traits in sport horses. In this study, we conducted a haplotype-based genome-wide association study (GWAS) for 36 conformation and free jumping phenotypes recorded during routinely conducted young horse evaluation tests involving 380 Swedish Warmblood (SWB) horses. The horses were evaluated by expert judges using both traditional and linear evaluation systems. All samples were genotyped using the 670K Affymetrix® Axiom® Equine Genotyping Array, haplotypes were first phased, and haplotype blocks were calculated for a total of 78,000 haplotypes. To assess the association between the haplotypes and studied traits, a single trait linear mixed model was used, correcting for sex and the date-location in which the evaluation took place. In the analysis, a total of 11 haplotype blocks were found to be significantly associated with a total of six traits: height at withers, the conformation traits hooves and correctness in movement, and the free jumping traits technique: haunches, carefulness, and distance estimation. In the proximity of those haplotypes (windows size ± 500 kb), 33 protein-coding genes, 31 IncRNAs, and one miRNA were found. Within those regions, key candidate genes were located such as LCORL and KHDRBS3, associated with body size and growth, as well as COL12A1, MYO6, and FILIP1, involved in musculoskeletal development and muscle elasticity and strength. The haplotype-based GWAS approach proved to be a useful method since it helped in the detection of aggregated genetic effects. Future studies with larger sample sizes and using novel tools for objective phenotyping will be essential to further investigate the genetic mechanisms behind sports performance.

Keywords: Association Study; Equine; Genomics; Haplotype; Performance.
Plain language summary

The Swedish Warmblood is a sport horse breed, valued for its performance, rideability, and temperament. To improve breeding, it is important to understand the genetic background of traits linked to sport performance. However, these traits are influenced by many genes, making them difficult to study. In this project, we analyzed the DNA of 380 young Swedish Warmblood horses, all evaluated by expert judges for conformation and free jumping ability. Using a haplotype-based genome-wide association study (GWAS), we grouped genetic markers into blocks (haplotypes) and tested their relationship with 36 traits. We found 11 genetic regions linked to six conformation traits: height at the withers, hoof quality, correctness of movement, and to three free jumping traits (technique in the haunches, carefulness, and distance estimation). Within these regions, we identified 33 coding genes and several non-coding RNA genes that may play a role in defining horse performance. This haplotype-based approach gave novel insights into the genetic background of sport performance related traits in horses. Future studies with more horses and advanced digital tools for measuring traits will help to further reveal the complex genetic basis of sport performance in horses.

© The Author(s) 2026. Published by Oxford University Press on behalf of the American Society of Animal Science.

• This topic was modified 1 month ago by Robert Oglesby DVM.
• This topic was modified 1 month ago by Robert Oglesby DVM.