Haplotype GWAS in Swedish warmblood horses for conformation and jumping traits

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.