Applied genetics - The Horse Owner's Resource

Applied genetics

Dozens of genetic tests are now available that can offer insights into equine health, coat color and even performance potential. Here’s what they can and can’t tell you.
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Turn on the radio or television and you can’t miss them: Advertisements for genetic testing are almost as common as commercials for laundry detergent and auto insurance. Just a decade or two ago, such ads were unheard of. Yet today, genetic testing services---for animals as well as people---are more numerous, more accurate, more affordable and more convenient than ever.

“What most folks don’t know about genetics is really how advanced it has become,” says Christa Lafayette, CEO of Etalon Inc. of Menlo Park, California. “Genetics is the new smartphone. Think back to when you first heard someone say, ‘There’s an app for that,’ and you had no concept as to what, exactly, an ‘app’ was. Now they are completely taken for granted and just common knowledge. That is where genetics is headed.”

The first genetic tests for horses became available in the 1990s, and for many years they were used only occasionally. Dozens of tests are now available. Most are being used in breeding decisions that will shape future generations of horses, but others offer insights into the health, beauty and potential of horses here today. As genetic tests become increasingly affordable and accessible, the role they will play in the horse world will only continue to grow.

Identifying inheritable diseases

Many inherited diseases result from single gene mutations that cause changes in how the body functions. The mutation is considered dominant if a foal needs to inherit only one copy of the defective gene to be affected by the disease. If the mutation is recessive, the foal needs to inherit two copies of the defective gene, one from each parent, to be affected. A horse with only one copy of the recessive gene is a carrier---he may be completely normal but is capable of producing a foal with the disease when mated to another carrier (see “Basics of Inheritance,” page 40). A mutation is considered incomplete dominant if a horse with one copy of the mu- tated gene is more mildly affected and a horse with two copies is more seriously affected.

Most tests for heritable diseases are breed specific, and some organizations require testing for particular genes prior to registering breeding stallions to limit the prevalence of certain conditions in the population.

Since 2015, for instance, the American Quarter Horse Association (AQHA) has required all registered breeding stallions to undergo a five-panel test for the following genetic diseases:

• glycogen branching enzyme deficiency (GBED), a fatal condition caused by the body’s inability to store glycogen, resulting in progressive weakness and organ failure

• hereditary equine regional dermal asthenia (HERDA), a connective-tissue disorder which causes fragile skin that tears easily and is so slow to heal and prone to infections that euthanasia is often the most humane option

• hyperkalemic periodic paralysis (HYPP), which is characterized by episodes of muscle weakness and tremors and, in severe cases, collapse and respiratory or cardiac failure

• malignant hyperthermia (MH), a condition in which extreme stress, exercise or anesthesia triggers muscle rigidity, fever, excessive sweating, shallow breathing and an irregular heart rate

• polysaccharide storage myopathy type 1 (PSSM1), which causes an abnormal accumulation of sugars in the muscles leading to cramping, tremors and characteristic dark urine as the kidneys flush the byproducts of muscle damage. Note: Although testing for PSSM1 is required for Quarter Horse breeding stallions, the disease has been found in more than 20 breeds, including several drafts and warm- bloods with European bloodlines as well as American stock horses.

In addition, a test can determine whether Quarter Horses carry the gene for androgen insensitivity syndrome, which causes males horses to have female physical attributes, but it is not required for registration of breeding animals.

Beginning January 1, 2018, the American Paint Horse Association will require all breeding stallions to undergo the genetic tests in the AQHA five-panel profile, plus one other, overo lethal white syndrome (OLWS), which produces foals who are born almost pure white and have undeveloped nerves in the intestinal tract, making it impossible to process food and pass feces. OLWS appears in Paint Horses as well as mustangs, Spotted Saddle Horses and any other breeds that can show a frame overo coat pattern.

While other registries may not require genetic testing for diseases right now, many other tests for breed-related conditions are available, including:

• congenital stationary night blindness (CSNB), which is limited or no nighttime vision caused by a gene linked to the leopard-spotted coat pattern. Leopard spots are best known as a breed-defining pattern in Appaloosas and Pony of the Americas but can also occur in other breeds such as the Knabstrupper, Noriker and some Spanish mustangs.

• junctional epidermolysis bullosa (JEB), which inhibits the production of proteins that help adhere the skin to the body, leading to blistering, sloughing of skin and fatal infections. JEB was first discovered in Belgians (Belgian-JEB); a form of the condition is also found in Saddlebreds (Saddlebred-JEB), although the genetic cause is different.

• severe combined immunodeficiency disease (SCID), which inhibits the body’s ability to produce white blood cells that play a vital role in immune functions, and lavender foal syndrome (LFS), which causes several neurological signs. Both of these are found in Arabians, along with cerebellar abiotrophy (CA), which causes the death of neurons in the cerebellum that affect balance and coordination, and is occasionally found in other breeds.

• ocular squamous cell carcinoma (SCC), a type of tumor that appears on the edges of the eyes and on the third eye- lid, in Haflingers

• warmblood fragile foal syndrome (WFFS), which causes fragile skin that tears easily and is slow to heal, lax joints that may prevent standing, and lesions within the mouth.

Knowing a horse’s genetic status can help an owner make more informed management decisions. If you know your horse is susceptible to ocular SCC, for example, you can make sure to protect him from sun exposure with a fly mask and take other precautions to try to prevent the condition or at least catch it early. Genetic testing is also becoming a common part of prepurchase exams.

While horse owners may find genetic tests useful, breeders are their primary users. By identifying stallions and mares with one copy of recessive genes associated with certain diseases, breeders can avoid mating carriers to other carriers to avoid producing affected foals.

But that doesn’t mean carriers can’t be bred at all---in many breeds, removing all carriers from the breeding pool would severely limit genetic diversity. “If we were to eliminate all horses that had one copy of one of the five-panel disorders, we would probably eliminate 30 to 40 percent of all American Quarter Horses, thus greatly reducing the gene pool,” says Arne de Kloet, director of Animal Genetics in Tallahassee, Florida.

By breeding carriers of undesirable genes only to noncarriers, breeders can avoid producing foals with recessive diseases while still preserving other desirable traits these horses may have. “Animal Genetics reports all SCID test results to the Arabian Horse Society,” says de Kloet. “Interestingly, the number of carriers we see is almost the same as it was 15 years ago, but the number of homozygous [horses with two copies of the mutation] positives we see is almost zero. This tells me people have been breeding smart. If I have a stallion that has one copy of SCID, I’ll never breed him to a mare that also has a copy of SCID, and we’ll never have a problem. This enables horses with many great qualities to remain in the breeding program.”

Currently, genetic testing is required only for Quarter Horse breeding stallions, but many breeders are opting to test prospective broodmares of the breed as well. “There is both breeder wisdom and market pressure pushing increased testing of mares,” says Cecilia Penedo, PhD, director of the Veterinary Genetics Laboratory of the University of California–Davis.

Even with the new information that genetic tests can provide, breeding decisions still require a balancing act. “Some mutations have been maintained for advantage,” says Kathryn Graves, PhD, director of the Animal Genetic Testing and Research Laboratory of the Gluck Center at the University of Kentucky. “The PSSM1 mutation may have given working draft horses superior abilities to pull or carry heavy loads. The mutation that has given us the beloved Appaloosa color pattern that can also be associated with night blindness, but do we want a world without Appaloosas? We have to be careful not to make our first response a rush to eliminate all mutations. The irony is that genetic testing is giving us new tools to undo the results of our own selective breeding.”

Colors, patterns and parentage

Genetic analysis isn’t all about health, though. Tests are also available that provide insight into your horse’s coat color, patterns and parentage ---traits that may seem obvious at first, but a peek at your horse’s DNA can reveal surprising or otherwise un-knowable information.

Testing can determine whether a horse carries one, two or no copies of the genes required for more than a dozen coat colors and patterns. These include

• base colors, which will be either black, red or bay.

• dilution factors, which are five testable genes that modify the color of the base coat. These are champagne, cream, dun, pearl and silver.

• patterns, which are genes that eliminate pigment and produce white hairs on the body, including dominant white, gray, tobiano, splashed white, overo, sabino, leopard complex and roan.

Tests for coat colors and patterns are relatively inexpensive, and they can be used by owners who simply want to know what color their horses are. Many coat colors can look very similar ---a palomino, for example, can be hard to distinguish from a silver-dappled bay---and if a horse’s parentage isn’t known, the only way to be certain is by a genetic test.

Mostly, however, genetic tests for coat colors and pattern are used by breeders who want to be able to predict what colors their mares and stallions can produce. This capability has both pros and cons, if too strong a focus on coat colors or patterns outweighs other desirable traits.

“There is a definite danger there,” Graves says. “We have seen this happen in some breeds already. For example, if a registry has strict color requirements and horses of any other color are excluded, the breed runs the risk of becoming inbred, which may bring consequences such as infertility or an increase in the prevalence of other undesirable genetic traits.”

These tests are more critical in the case of the frame overo pattern. Breeders need to identify horses who carry this mutation to avoid producing a foal with lethal white syndrome. One of the splashed white genes may also produce lethal white foals, but that connection has not been proven.

Finally, confirming parentage of a horse was one of the original uses of genetic testing and remains one of the most common. A number of breed organizations require that foals have their parentage confirmed before they can be registered. These tests require the submission of hair samples pulled from the foal as well as from both his sire and dam. If the sire is uncertain, then samples can be submitted from all possible sires.

By comparing inheritable traits in the DNA, these tests can confirm a foal’s parentage with efficacy greater than 99 percent; an incorrect sire can also be excluded with 100 percent certainty. “We compare the genetic profile of the sample of mane or tail hair submitted to our database profiles of the sire and dam,” Graves says. “We verify the parents and send those reports to the registries.” However, these tests do not reveal the breed of an individual horse.

Owners seeking to register their horses are the most common users of equine genetic testing. “The DNA test for parentage verification represents the largest number of samples tested,” Penedo says. “Most horse breed registries now require DNA testing for registration, which translates to hundreds of thousands of horses being tested yearly around the world.”

What lies ahead?

Like many other technologies, genetic testing is becoming faster, more affordable and thus more accessible. “The cost of sequencing a horse’s entire genome is coming down,” Graves says. “Today, this can be done for about $8,000 to $10,000. Soon, perhaps within 10 years, it will cost only about $1,000. At that point, the average horse owner will be able to sequence her horse’s entire genome.”

The challenge, says Graves, will be determining how best to use this information. “We still have a lot of work to do before we will know that,” she says. “We need to create maps of each breed of horse. This will enable us to look for desirable performance traits or for genetic anomalies in a horse that has chronic health problems.”

Could genetically engineered “super horses” appear in the future? Possibly, with a new technology called “gene editing,” which Penedo describes as using “molecular scissors” to insert, remove or replace DNA sequences in the laboratory. “I can envisage that it will be tried in horses, but given the costs it is unlikely to become common practice,” she says. One application of this technology that she does foresee, however, “would be to correct the DNA sequence in an early embryo from highly valuable parents that is affected with a genetic defect, as determined from pre-implantation embryo genetic testing. The expectation is that the defective gene could be replaced by a normal gene, and the ‘edited’ embryo could then be implanted.”

In the meantime, the number of specific tests available---both for diseases as well as other aspects of a horse’s health and physiology---will likely continue to grow as researchers learn more about equine genetics. “It is a constantly evolving field,” de Kloet says. “Just as with human genetics, it’s going to change and evolve in the number of tests available and with regard to how the testing is being done. We have software programs and the computer ability to go through and look at a billion nucleotides in only a couple of days.”

To help with further research, Etalon Diagnostics offers several tests to the public, for conditions such as lordosis (“swayback”), that are in the “discovery stage”---that is, although there is some evidence of genetic factors for these conditions, the results of these specific tests have not been fully validated by research studies. Etalon’s goal is to gain feedback from owners to help support the research.

“Our platform is collaborative, meaning that it relies in part on feedback from horse owners,” Lafayette says. “We look for associations between certain genetic mutations and performance or other health traits based on emerging research data. When we see a pattern that suggests a genetic link, we follow up with horse owners and track the input we receive from them. This leads to the discovery or confirmation of connections between genetic mutations and resulting traits faster than would be possible if we were to go the conventional research grant route.”

Lafayette admits, however, that this approach is still a work in progress: “Since this kind of horse- owner-driven research platform has never been attempted before, the learning curve is steep,” she says. “We have to continually adjust our methods, studies, and the way we approach and present the information.”

The demand for genetic testing is already large and is likely to continue to grow in the coming years as the technology develops and new tests become available. Already, says Lafayette, labs like hers are receiving all kinds of requests from people who want more information about their horses: “Big ones, little ones, wild ones and pocket ponies, all colors, all disciplines. People want to know everything from color and health to speed and gait. Folks are excited to talk and learn more about their horses, as are we.”

This article first appeared in the August 2017 issue of EQUUS (Volume #379)

SIDEBAR

Performance and personality testing

While genetic tests for diseases, colors and parentage can provide DNA “proof” of a condition, those looking for genes associated with performance-related traits yield less definitive information. How or whether these genes are expressed can be influenced by training, environment and other factors.

For instance, performance testing, aimed primarily at Thoroughbreds, looks at multiple genes to attempt to predict a horse’s speed, stamina and overall potential for success at the racetrack. One factor these tests analyze is the myostatin gene, which controls the amount of muscle mass developed. Other components of the tests may predict a foal’s height at maturity as well as whether he will do better on dirt versus turf tracks.

Gait testing identifies a mutation on the DMRT3 gene that influences a horse’s ability to perform lateral gaits. The mutation is recessive—horses with two copies of the gene are common in Icelandic Horses, Paso Finos, Tennessee Walking Horses and other gaited breeds. The effects of carrying only one copy of the mutation varies by breed, but those horses generally perform the lateral gaits with less speed and facility.

Having a particular “performance” gene isn’t a guarantee, however. After all, many a racing phenom has had full siblings who washed out at the track, and every so often a horse with a modest pedigree takes the show world by storm. DNA is only part of the equation.

Another test, described by its manufacturer as “curiosity vs. vigilance,” analyzes a mutation that affects dopamine0 receptors in the horse’s brain. Horses with two copies of the recessive gene are defined as more curious—that is, more inclined to take an interest in and approach new objects. Horses with only one or no copies of the gene are more vigilant, or less inclined to explore their surroundings.

“An oversimplified example of this might be that horses who test positive for ‘curiosity’ might outperform those who do not in, say, a trail competition,” says Christa Lafayette, CEO of Etalon Inc. of Menlo Park, California, who adds that the real utility of the test will only be known once owners begin interpreting the results. “It’s going to be interesting to see what owners say about it and whether or not they find a correlation between curiosity/vigilance and certain types of activity.”

This article first appeared in the August 2017 issue of EQUUS (Volume #379)

Answers about ancestry

For as much as equine genetic testing has expanded over the years, one type of test isn’t available yet. “We don’t yet have a test that can tell us what breed or mix of breeds is in an individual horse,” says Kathryn Graves, PhD, of the Gluck Center at the University of Kentucky. “We would be very popular if we could offer this test, because we get requests for it several times each week.”

The challenge is that many of our modern breeds descend from the same foundation stock, and researchers don’t yet have enough genetic profiles of individual horses of different breeds to be able to distinguish them. “While breed identification of purebred horses is more easily done, determination of breed contributions in crossbred horses is a far more complex problem,” says Cecilia Penedo, PhD, of the University of California–Davis. “Perhaps in the near future, this limitation may be overcome by careful selection of DNA markers for breed composition tests to become more informative and accurate.”

This article first appeared in the August 2017 issue of EQUUS (Volume #379)