10 Things You Might Not Know About Equine Genetics

courtesy of UC Davis School Of Veterinary Medicine

1. DNA is found in the nucleus of cells. Samples submitted for genetic testing are usually hair, blood, or tissue. Hair samples must contain the “bulb”, which looks like a tiny ball at the root of the hair. This is where the DNA is located. When submitting hair samples, make sure to pull, not cut, the hairs so the bulb is present. Blood and tissue samples require additional steps, such as an anticoagulant (for blood) or freezing (for tissues). Always follow the testing laboratory’s instructions for sample submission and contact them with questions.

2. There is no age limit for DNA testing. An animal’s DNA profile does not change over time, so a horse can be reliably tested at any age. Genetic tests can be performed for foals, but it is recommended to submit 30 – 50 tail hairs since the bulbs on foal hair are smaller than adults and more are needed.

3. Parentage testing is based on exclusion. The offspring, dam, and potential sires are tested for a number of markers, and the offspring is compared to the potential parents for each marker. The offspring must have received one allele for each marker from each parent. It is possible to do parentage testing with a sample from only one parent (~95% accuracy), but results are more accurate (>99%) with both. Accuracy will decrease when the potential parents are part of a large group of closely related animals.

4. SynchroGait™ tests for a genetic variant that facilitates lateral gaits (ambling and pace). Owners can use this test to identify the natural ability of young horses for gait performance, and use the results to make training decisions. Breeders can use the test to select for or against this mutation, depending on what is desirable in their chosen discipline.

5. Horses have 3 base coat colors that are controlled by the interaction of 2 genes. The coat colors chestnut, bay, and black are determined by horses’ genotypes at the MC1R gene (extension (E) locus), which controls the production of red and black pigment, and the ASIP gene (agouti (A) locus), which controls the distribution of black pigment to the mane, tail, lower legs, and ear rims (points), or uniformly over the body.

6. Dilution factors modify base coat colors. These include cream, champagne, dun, pearl, silver, and mushroom. The resulting coat color depends on the combination of the base color genotype and the dilution factor genotype. For example, a horse with one copy of the cream allele on a chestnut base color will be palomino whereas on a bay base color it will be buckskin. Modes of inheritance and causative mutations have been identified for these dilution factors, and genetic testing is available. For more on the basics of horse coat color, the Veterinary Genetics Laboratory provides an online guide to equine coat color genetics.

7. Horse size is highly heritable. Height in horses is determined by the interaction of genetic and environmental factors (such as nutrition). Four genetic variants have been identified that account for >80% of horse height. One variant has a particular influence on height in warmbloods and a different variant has a strong influence on height in Shetland ponies and miniature horses. Mutations related to dwarfism have also been identified in some breeds (dwarfism in Friesians, skeletal atavism in Shetland ponies and American Miniature horses). Additional unidentified genetic variants that influence height in horses are likely.

8. Equine genetic ancestry tests are available, but there are a few things to keep in mind. Equine ancestry tests, or “breed prediction” tests, compare a horse’s DNA to horses in a reference panel. Results are dependent upon the breeds and number of horses of each breed in that panel (which can vary by test provider). Some horse breeds are not very genetically distinct from one another, and many breeds have influenced the creation of other breeds, which can complicate results. These tests can report the probability that a certain breed is an ancestral breed for a horse, but not the proportion or percent of that breed in a horse’s genetic makeup. The larger the number of breeds involved in a cross, the lower the probability of a clear result.

9. Genetic testing can be performed for embryos. Embryos recovered from uterine flushes as part of embryo transfer procedures can be tested to determine gender and genetic traits prior to implantation in the recipient uterus. This allows for selection of embryos that have the desired sex, coat color variants, or that are free of known genetic diseases

10. In the future, horses will be able to have their entire genome sequenced. Whole genome sequencing of modern and ancient horses has provided a wealth of information to researchers. As this technology becomes more affordable (currently ~$1600 per animal), whole genome sequencing of individual horses is likely to become more accessible. Coupled with advanced knowledge in equine health, whole genome sequencing will provide veterinarians, owners, and breeders with a powerful tool to tailor training, management, and health care to the individual animal.