Exploring the Genetic Regulation of Ability and Quality of Gaits in Icelandic Horses
Authors: Sigurðardóttir Heiðrún 
Published: January 2025

The Icelandic horse is celebrated for its unique gaits and versatility as a riding horse, yet the genetic basis of these characteristics is not fully understood. Its diverse gait range, the availability of extensive phenotypic records, and the application of advanced genomic technologies make the Icelandic horse an invaluable model for exploring the genetic foundations of gait traits and performance.
This thesis aimed to identify novel genetic factors affecting gaits and performance in the Icelandic horse by integrating genomic approaches to analyse genetic variation through genome-wide patterns of homozygosity and polymorphic variation. The study utilized high-density SNP genotype data, generated using a 670k genotype array, from 380 horses to perform genome-wide association (GWA) studies and runs of homozygosity (ROH) analyses. Additionally, 39 horses were included for whole-genome sequencing (WGS) analysis.
Through GWA studies, quantitative trait loci (QTLs) affecting gait traits were identified. One QTL was associated with breeding scores for back and croup conformation, which significantly influenced the quality of the lateral gaits tölt and pace. Two additional QTLs were directly linked to breeding scores for pace. Haplotype analysis revealed two frequent haplotypes for each identified QTL that had significant effects on the associated trait. The haplotypes associated with back and croup harboured genes with known roles in muscle and skeletal development in humans. The haplotypes affecting pace scores were located within the candidate genes STAU2 and RELN which are expressed in neural tissue. In addition to the observed effects on pace, the STAU2 haplotypes were found to significantly influence the quality of trot and gallop, while the RELN haplotypes impacted the quality of tölt, trot, canter, and gallop, and may potentially also influence the trainability and precocity of young horses. Moreover, interactions between STAU2, RELN, and the previously identified DMRT3 gene were observed, involving both additive and compensatory effects. Sequence analysis in these regions revealed a partial loss of the STAU2 protein caused by a one-base-pair frameshift insertion. This variant was proposed to be causative for the observed effects of the STAU2 haplotypes. In the RELN region, potential regulatory elements were identified and suggested as candidate variants influencing the effects of the RELN haplotypes.
The enduring significance of the genomic region on ECA23, harbouring the DMRT3 gene, was confirmed through ROH analysis, while additional regions of potential relevance to performance traits were identified. Analyses of genomic inbreeding and genetic diversity indicated that recent breeding practices in the Icelandic horse breed have been sustainable, maintaining adequate genetic diversity.
In conclusion, this thesis expands current knowledge of the genetic basis of gait and performance in the Icelandic horse, by demonstrating that genetic factors beyond DMRT3 contribute to the regulation of gait ability and quality. The findings warrant further investigations and may ultimately benefit the breeding of the Icelandic horse and assist breeders in making more informed breeding decisions.