# Two Cases of Chromosome 27 Trisomy in Horses Detected Using Illumina BeadChip Genotyping

## TL;DR

This study identifies two cases of chromosome 27 trisomy in horses using SNP genotyping, showing how genetic testing can detect rare chromosomal abnormalities that may otherwise go unnoticed.

## Contribution

The study presents the largest population-level screening for autosomal trisomy in horses using SNP genotyping data.

## Key findings

- Two Irish Sport Horse colts were found to have trisomy on chromosome 27, with a prevalence of 0.03% in juveniles.
- One colt showed no external abnormalities, highlighting the need for genetic testing for accurate diagnosis.
- Heterodisomy was observed in both cases, likely due to nondisjunction during meiosis in the parents.

## Abstract

The presence of an extra autosome (i.e., autosomal trisomy) is rare in equine populations and is often associated with infertility, developmental anomalies, or early mortality. However, not all trisomies manifest with overt phenotypic abnormalities, making diagnosis challenging without specialized lab testing (i.e., cytogenetics) or molecular analysis. Using single nucleotide polymorphism genotype intensity data from 17,078 horses, two Irish Sport Horse colts were diagnosed with trisomy on chromosome 27, representing a prevalence of 0.03% in a juvenile population. One colt showed no external abnormalities and would likely have gone undiagnosed without genetic testing. As SNP genotyping becomes more common in sport horse registries, it offers a cost-effective opportunity to screen for chromosomal abnormalities early in life, potentially reducing future issues for breeders and owners.

Autosomal trisomy, a genetic disorder characterized by the presence of an extra autosome, is a rare but important chromosomal abnormality in horses, often associated with infertility, developmental abnormalities, and reduced life expectancy. This study represents the largest population-level screening for autosomal trisomy in horses; the analysis used single nucleotide polymorphism (SNP) panel genotype intensity data from 17,078 horses, 6601 of which were juveniles (i.e., ≤12 months of age) when genotyped. Using methodologies adapted from similar screening studies in cattle, the only aneuploidy detected was trisomy 27 in two juvenile male Irish Sport Horses (ISH) (0.03% prevalence among juveniles or 0.01% prevalence in the overall population). One ISH colt was cytogenetically confirmed and displayed no overt external phenotypic abnormalities, while cytogenetics was not undertaken on the other ISH colt, nor was it phenotypically assessed. Parentage analysis revealed that one ISH colt inherited two different copies of chr27 from the sire, demonstrating heterodisomy, likely due to a nondisjunction event during meiosis I in the sire. The other ISH colt inherited two different copies of chr27 from the dam, also indicating heterodisomy; the dam was 23 years of age when the colt was born. Based on the observed prevalence of autosomal trisomy, it can be estimated that at least 3 foals per 10,000 live births are likely to have autosomal trisomy. Though, given that only 74 (i.e., 0.004%) of horses were genotyped within a month of birth, this is likely an underestimate. The economic consequence of undiagnosed trisomy in high-value breeding horses that are potentially infertile could be substantial. As horse genotyping for parentage verification and discovery is transitioning to medium-density single nucleotide polymorphism panels, routine genomic screening for autosomal aneuploidy could be readily undertaken and potentially should form a standard screening prerequisite along with other genetic defects at horse sales. Currently, thoroughbred horses registered for racing are not genotyped, and only a limited number of sport horse studbooks are using SNP genotyping. This highlights an opportunity for those already genotyping to expand their support for breeders through low-cost, high-value chromosomal screening at the time of registration rather than incurring additional costs over the horse’s life cycle to determine the root cause of certain phenotypes owing to the undiagnosed trisomy.