DMRT3 gene variations in horse breeds selected for gaited movement - established research and novel findings

The DMRT3 gene, often referred to as the "gait keeper," plays a key role in controlling alternative gaits in horses, such as tölt and pace. This study aimed to determine the frequency of known and to screen for potential novel polymorphisms within the second exon of the DMRT3 gene.

A total of 244 blood or hair samples were collected from representative individuals of the six horse breeds: gaited (Icelandic Horse, French Trotter), non-gaited (Arabian Horse, Malopolski Horse), and pony breeds (Welsh Pony, Shetland Pony).

The second exon of the DMRT3 gene analyzed using Sanger sequencing. Detected polymorphisms were annotated and classified using Ensembl and NCBI databases. Allele frequencies and genotype distributions were statistically compared between breeds and breeding populations. Putative novel variants were further analysed using in silico approaches to predict their potential structural and functional consequences at the protein level.

Six polymorphisms were identified, including three novel variants. The known stop-gain variant c.902C>A (DMRT3_Ser301STOP) was confirmed in Icelandic Horses and French Trotters, with significant genotype differences between two French Trotter studs (p < 0.05). A novel 18-nucleotide in-frame duplication (c923_943dup; Ala297_Ala302dup) was found exclusively in Shetland Ponies. Additionally, a missense variant (c.967T>A; p.Tyr323Asn) and a synonymous change (c.855T>C) were detected in non-gaited breeds. In silico analyses suggested no major structural impact of the identified variants on the predicted DMRT3 protein.

This study confirms the distribution of the DMRT3_Ser301STOP allele in gaited breeds and identifies novel polymorphisms in DMRT3. It expands current knowledge by identifying population- and breed-specific variants, suggesting a broader genetic influence on locomotor traits beyond gaited horses. The findings support the continued identification of DMRT3 as a molecular marker in equine locomotion research and selective breeding.