Horse Sport Ireland Publishes Second Research Paper Using SNP Genotypes

Horse Sport Ireland is pleased to announce the publication of its second research paper utilising SNP (single nucleotide polymorphism) genotypes detecting equine trisomy, further strengthening Ireland’s leadership in equine genomic research.

This study was conducted in collaboration with researchers from Teagasc, South East Technological University, the University of Agriculture in Krakow, and Texas A&M University. It focuses on the identification of horses with autosomal abnormalities using the SNP genotypes collected from Irish sport horses during the parentage verification process.

The research, titled “Detection of Two Horses with Chromosome 27 Trisomy Using Single Nucleotide Polymorphism Chip Genotypes”, has been published open-access in the journal Animals and is available to read HERE.

Autosomal trisomy is a rare genetic disorder caused by the presence of an extra chromosome. While well-known in humans (e.g., Down syndrome (trisomy 21), Edwards syndrome (trisomy 18), Patau syndrome (trisomy 13), its occurrence in horses is uncommon but can lead to developmental abnormalities, infertility, and reduced life expectancy.

This study represents the largest population-level screening for autosomal trisomy ever conducted in horses, analysing 17,078 animals. From a subset of 6,601 juvenile horses, two Irish Sport Horse colts were identified with trisomy of chromosome 27. One of these was examined and showed no obvious physical abnormalities, but the diagnosis was confirmed via cytogenetic analysis.

The findings estimate that at least 3 in every 10,000 live foal births may be affected by autosomal trisomy—an often-undiagnosed condition without genetic screening. For high-value breeding horses, the economic impact of undetected abnormalities related to fertility or development could be significant.

Horse Sport Ireland and its research partners hope this study will raise awareness of the value of routine genomic screening for chromosomal abnormalities, particularly where studbooks are already using SNP-based parentage verification.

This marks the second collaborative publication between HSI and Teagasc within the past 12 months. The same research team—Dr. Jennifer Doyle, Dr. Sonja Egan, and Dr. Donagh Berry—also authored Horse Sport Ireland’s first-ever published research paper: “Imputation of Single Nucleotide Polymorphism Genotypes in Ungenotyped Sport Horses from the Genotypes of Their Progeny.”

Dr. Jennifer Doyle, HSI Senior Geneticist and Senior Author on the paper: “I’d like to thank all our collaborators on this project, especially Dr. Cliona Ryan of Teagasc, for her dedication and hard work. This research is a vital contribution to equine health and fertility, demonstrating the broader potential of SNP genotyping. It highlights how this technology can support breeders and veterinarians in making informed decisions.”

Dr. Sonja Egan, HSI Head of Breeding Innovation and Development and Co-author: “When we began the SNP transition in 2022, we knew the benefits for Irish breeders would be substantial. Today, Horse Sport Ireland is recognised as a leader in SNP implementation and research — first through the publication of validated SNP-SNP imputation in horses, and now with the largest genomic screening for equine trisomy ever conducted. These advancements are already being applied in real time to improve registrations and support diagnosis of rare conditions that would otherwise go undetected. Importantly, identifying a rare chromosomal condition doesn’t mean the population is flawed — it means we have the tools and transparency to protect breeders. If a testing system never finds anything, it’s probably not looking.”

These results highlight the advantage of a strategically designed national SNP programme, where each DNA sample supports not only parentage verification, but also broader genomic screening, research, and long-term breed development. By ensuring every genotype serves multiple purposes, Horse Sport Ireland reduces duplication for breeders, delivers maximum value from each sample collected, and significantly lowers the cost of accessing advanced genetic tools.

For breeders, this means better outcomes at lower cost — all while contributing to the ongoing genetic improvement and health monitoring of the population.

Horse Sport Ireland would like to thank its research partners at Teagasc, South East Technological University, the University of Agriculture in Krakow, and Texas A&M University for their invaluable contributions. We also gratefully acknowledge the Department of Agriculture, Food and the Marine for funding the SNP transition process through the National Breeding Services fund.

Finally, we extend special thanks to the breeder who generously facilitated the case study by allowing access to the affected colt. Their contribution has been critical in advancing the understanding of equine trisomy and will undoubtedly help future cases be diagnosed more quickly and cost-effectively.

This research was part funded under National Breeding Services by the Department of Agriculture, Food and the Marine.

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