Why We Don’t Test for Certain Equine Genes: A Focus on Ethics and Evidence

New discoveries about inherited traits, colors, and disorders are exciting in the ever-evolving world of equine genetics - we would know! As a company dedicated to helping horse owners make informed breeding and management decisions, we take our responsibility seriously when deciding which genes to include in our DNA tests. Recently, there has been increased interest in testing for genes suspected to be associated with coat color such as roan, and health conditions such as Equine Juvenile Spinocerebellar Ataxia (EJSCA) and additional types of PSSM. However, we believe that genetic testing must always be grounded in sound scientific evidence, and in some cases, that evidence simply isn't there—yet.

The Role of Clinical Validation in Genetic Testing

Genetic testing provides valuable information, but only when backed by rigorous clinical evidence. Clinical validation is the process that confirms a genetic test’s ability to accurately predict, diagnose, or understand the development of a disease or condition. Without this validation, test results can lead to misleading or harmful outcomes.

Unfortunately, in the cases of EJSCA, PSSM type 2, and roan coloring, the genetic markers associated with these conditions have not yet undergone the clinical testing needed to validate them. While research is ongoing, Etalon believes in proven research done through robust, peer-reviewed clinical studies prior to offering tests for colors, traits, or conditions.

Genetic Testing for Equine Juvenile Spinocerebellar Ataxia (EJSCA)

Equine Juvenile Spinocerebellar Ataxia (EJSCA) is a condition of interest in the genetic testing world at the moment, especially amongst Quarter Horse breeders. EJSCA is a rare, inherited neurological disorder that affects young horses, typically within the first year or two of life. The condition is characterized by progressive degeneration of the spinocerebellar tracts, which is responsible for coordinating movement and balance. A scientific paper is currently in progress describing the gene associated with EJSCA and its corresponding genetic mutation. However, this research has yet to be published and undergo the peer review process, which is essential for validating any genetic test.

Until the scientific community has had the opportunity to thoroughly examine and validate this research, we believe it would be premature—and unethical—to offer a commercial test for EJSCA. Testing for a gene without published, peer-reviewed evidence supporting its association with the disease can result in false conclusions, misinterpretation of results, and poor decision-making by horse owners.

Moreover, providing a test based on unpublished data could harm the credibility of genetic testing as a whole. As a company dedicated to accuracy and ethical testing, Etalon is committed to waiting for the scientific process to run its course. When the research is validated, we will carefully and happily review it to determine whether it meets the standards necessary for inclusion in our testing panels.

Genetic Testing for PSSM Type 2 One condition that has generated significant attention in recent years is Polysaccharide Storage Myopathy (PSSM), particularly its type 2 variant. PSSM is a type of muscle disorder in horses that affects their ability to store and utilize glycogen, a form of stored carbohydrate. Type 1 is linked to a genetic mutation in the GYS1 gene, which is involved in glycogen synthesis. This mutation leads to an abnormal accumulation of polysaccharides in the muscles, which can cause muscle stiffness, pain, and poor performance. PSSM type 1 is well understood, and a genetic test is available to identify horses carrying this mutation.

PSSM type 2 is less understood as compared to PSSM type 1. Unlike PSSM type 1, PSSM type 2 does not yet have a single identified genetic mutation. It is characterized by similar symptoms to PSSM type 1, including muscle stiffness, soreness, and poor performance, but the underlying cause is unknown. The condition is diagnosed based on clinical signs and muscle biopsy findings, rather than a specific genetic test.

We hold Dr. Stephanie Valberg, a leading researcher on PSSM, in high regard as the foremost authority on this condition. Dr. Valberg’s research, published in the Equine Veterinary Journal, did not find a correspondence between commercial PSSM type 2 genetic testing and histopathological diagnosis (muscle biopsy findings) in horses suspected of having the condition.¹ This lack of alignment between the test results and clinical diagnosis raises significant concerns about the validity of these commercial tests for PSSM type 2.

As noted in the study, the commercial genetic markers currently offered for PSSM type 2 have not been scientifically validated through controlled studies, and offering these tests without such validation can lead to misdiagnosis and confusion among horse owners and veterinarians. You can find Dr. Valberg’s study here.

Testing for a Roan Color Gene

The roan color trait has also been a topic of interest in the equine genetics field. Roan in horses is characterized by an even blend of white and colored hairs, while the head, mane, tail, and lower legs remain solid in color. It can be combined with any base coat color to produce different shades. Despite ongoing research, the specific genetic mutation responsible for the roan coat color has not yet been clearly identified. Several studies have examined the genetic basis of the roan color, but the evidence remains inconclusive.

For example, a study from 1984 described an association between roan coat color and Extension, which determines a horse’s base color, but did not actually identify a precise mutation.² Another study in 1999 investigated roan’s potential genetic underpinnings, pinpointing the KIT gene as a potential source of roan, but again did not definitively locate the mutation responsible.³

A more recent study, published in 2020, also explored the genetic basis of roan color and found a relationship between a KIT mutation and roan in Icelandic horses, but could not provide definitive evidence linking that specific mutation to the trait in other populations.⁴ This study highlights the ongoing uncertainty in identifying the precise genetic cause of the roan coat color.

These studies highlight that while research is progressing, no clear, validated genetic test exists for roan color at this time. Offering a test based on incomplete or inconclusive data could mislead horse owners and breeders. Therefore, we choose not to offer a test for roan color until a specific, validated mutation is identified and confirmed through peer-reviewed research.

A Lack of Clinical Information is Not Definitive

It’s important to recognize that the absence of clinical validation doesn’t necessarily mean the genetic markers associated with these conditions are irrelevant. It simply means that we do not yet have enough scientific data to determine their significance. More research is needed to understand how these genetic markers function and their correlation with disease development in horses.

It is critical that genetic tests are both scientifically and ethically sound. Offering tests without sufficient clinical validation can cause confusion, lead to incorrect decisions regarding a horse’s health, or even stigmatize certain breeds or bloodlines unfairly. While some labs may be eager to offer tests based on early-stage findings, we believe it is crucial to wait until there is a strong, scientific consensus.

The Ethical Responsibility of Genetic Testing

At the core of our testing philosophy is the principle of ethical responsibility. Testing for genes with associations that have not been validated can create unnecessary anxiety for horse owners and breeders. If a genetic marker has not been proven to contribute directly to a disease or condition, how can we responsibly provide test results that suggest otherwise?

Offering a genetic test without clear evidence is not only scientifically unsound but also poses an ethical dilemma. We risk providing results that could lead to poor decisions, such as retiring an otherwise healthy horse or excluding a valuable genetic line from breeding. These consequences could arise from incomplete or misinterpreted data, causing unnecessary harm to both horses and the equine community.

Moving Forward: Prioritizing Evidence-Based Testing

We believe genetic testing should always be a tool for clarity, not confusion. That’s why we prioritize evidence-based testing protocols that have undergone the rigorous clinical validation necessary to provide meaningful insights into a horse’s health. As more research is conducted, and as our understanding of genetically linked colors, traits, and conditions grows, we will continue to evaluate the scientific data. We will gladly reconsider our stance if and when these genetic markers are validated through appropriate studies.

Etalon remains committed to ensuring that our tests provide reliable, actionable information that benefits the equine community and supports responsible breeding and management practices.

Conclusion

While genetic testing holds tremendous potential for the future of equine health, it must be approached with caution, care, and a commitment to ethics. By waiting for solid clinical evidence before offering tests for any condition, trait, or color, we ensure that we are providing the highest standard of genetic testing available today. We believe that this is the most responsible and ethical approach for the well-being of horses and the peace of mind of their owners.

References

¹ Valberg, S. J., Finno, C. J., Henry, M. L., Schott, M., Velez-Irizarry, D., Peng, S., McKenzie, E. C., & Petersen, J. L. (2021). Commercial genetic testing for type 2 polysaccharide storage myopathy and myofibrillar myopathy does not correspond to a histopathological diagnosis. Equine Veterinary Journal, 53(4), 690-700. https://doi.org/10.1111/evj.13345

² Sponenberg, D. P., Harper, H. T., & Harper, A. L. (1984). Direct evidence for linkage of roan and extension loci in Belgian horses. The Journal of heredity, 75(5), 413–414. https://doi.org/10.1093/oxfordjournals.jhered.a109968

³ Marklund, S., Moller, M., Sandberg, K., & Andersson, L. (1999). Close association between sequence polymorphism in the KIT gene and the roan coat color in horses. Mammalian genome : official journal of the International Mammalian Genome Society, 10(3), 283–288. https://doi.org/10.1007/s003359900987

⁴ Voß, K., Tetens, J., Thaller, G., & Becker, D. (2020). Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses. Genes, 11(6), 680. https://doi.org/10.3390/genes11060680