Genetic Testing: Black, White, or Shades of Gray?

Learn details about five-panel genetic testing and its positive influence on breeding decisions.

In the late 1980s, a mysterious disease ROCKED the Quarter Horse world, as well as breeds crossed with Quarter Horses. Horses suffering muscle tremors, weakness, collapse, and even death made headlines when the cause was traced to a genetic disease attributed to a prominent Quarter Horse bloodline. When researchers announced that HYPP (hyperkalemic periodic paralysis) linked to one very famous stallion named Impressive, there was an uproar in breeding barns across the country.

[READ: To Breed or Not To Breed]

A decade later breeders began to accept the importance of reducing the spread of this deadly disease. In 1998, the American Quarter Horse Association adopted a rule requiring all foals descending from Impressive to be tested for HYPP, with results listed on their registration papers. In 2007, horses carrying two genes for this disease were no longer accepted for registration. This marked the beginning of genetic testing and AQHA’s efforts to minimize the spread of genetic diseases within the breed.

Fast-forward to 2019. Genetic tests are now available for five different heritable diseases that’ve been identified in Quarter Horses and other stock breeds.

Here, I’ll explain what the five-panel genetic test is all about. First, I’ll give you a primer on basic genetics so you can understand how genes are inherited. Then, I’ll teach you the basics about the five different diseases that make up the five-panel genetic test. With this information, you’ll better understand how testing can help you make informed breeding decisions.

Genetics 101
When egg and sperm get together to create a foal, there’s a lot going on behind the scenes. Size, color, temperament—even some aspects of health—are pre-determined by the way traits passed from the mare and stallion combine. The science behind all of this is called genetics, and it’s a complex, fascinating process. Here’s how it works.

Every horse has, within each cell, 32 pairs of chromosomes that contain all of the genetic information that makes him what he is. One set of these pairs came from his dam via the egg, the other from the stallion via the sperm. These chromosomes carry more than 30,000 genes, or specific messages, that determine different traits.

Genes can be either dominant (they’re expressed even if carried on only one set of chromosomes) or recessive (a matching pair must be present to have the trait in question). Some genes have incomplete dominance, meaning the trait is exhibited most strongly if both sets of genes are present, but can still be present even if there’s only one gene there. Here’s an example of how it works.

Pretend that the trait for patience is a dominant trait—symbolized by a capital P. A small p means your stallion (or mare) doesn’t carry the patience gene. Your stallion gets one gene from his dam, and one from his sire. The following combinations can result.

Combination 1: PP. Your stallion got a patience gene from each parent, so is homozygous for patience. Not only will he stand in the crossties for hours without complaint, but if he’s bred, he’ll pass on a patience gene to his offspring, too.

Combination 2: Pp. Your stallion got a patience gene from one parent, but not from the other. He’s heterozygous for patience. Because the gene is dominant, he’ll still be patient. If the patience gene had incomplete dominance, he’d be patient—just not quite as patient as he would be if he were PP. If he’s bred, only half of his offspring will get the patience gene from him. The other half will depend on their dams to determine whether they’ll be patient.

Combination 3: pp. Your stallion is homozygous recessive when it comes to the patience gene. He’s not patient at all, and his offspring will only be patient if they inherit a patience gene from their dams.

Now let’s change our scenario, and pretend that the patience gene is recessive—meaning it’s only expressed if both genes are present. In this situation “p” would stand for patience, and your stallion will only be patient with Combination 3 (pp). Although he’d carry the gene in Combination 2 (Pp), no one would know he had it, because he wouldn’t be patient at all. Half of his offspring would inherit the gene, but they’d only be patient if they inherited another patience gene from their dams (making them pp). And if your stallion were PP, there’s no chance any of his offspring would be patient.

The Five-Panel Genetic Test
Now let’s take a look at the five heritable diseases identified in stock breeds and tested for with the five-panel genetic test. These include hyperkalemic periodic paralysis (HYPP), polysaccharide storage myopathy (PSSM), glycogen branching enzyme disease (GBED), hereditary equine regional dermal asthenia (HERDA), and malignant hyperthermia (MH).

Hyperkalemic Periodic Paralysis (HYPP)
This disease causes a dysfunction of the channels, or pathways, that sodium passes through into and out of muscle cells. This disrupts the conduction of impulses that stimulate muscle contraction and can lead to episodes of muscle tremors, weakness, cramping, and collapse. In severe cases, an HYPP episode can be fatal.

How is it inherited? HYPP is a dominant gene, with incomplete dominance. This means your horse is likely to be severely affected if he’s homozygous (carries two genes for the trait), and less severely affected if he is heterozygous (carries only one gene for the trait). If he’s homozygous for the trait, all of his offspring will have the disease—but its severity will depend on whether they inherit a gene from their dam. If he’s heterozygous, he’ll only pass on the gene to 50 percent of his offspring.

How common is it? While estimates say that only 1.5 percent of Quarter Horses carry this gene, its incidence in halter horse bloodlines is a staggering 56 percent.

Hereditary Equine Regional Derma Asthenia (HERDA)
This skin disorder is caused by an abnormality in collagen, a protein described as the “glue” that holds connective tissues together. Any kind of pressure can cause the outer layer of an affected horse’s skin to split away from the layer beneath it—resulting in severe damage and scarring. Most commonly, damage is seen in areas where tack rests, such as on the back or under bridles and breast plates.

How is it inherited? HERDA is a recessive trait, meaning your horse must be homozygous for the condition (have two copies of the gene) to be affected. However, if your horse is heterozygous (has only one copy of the gene), he’s a carrier, meaning he won’t show any symptoms at all but can still pass the gene to his offspring.

How common is it? It’s estimated that 3.5 percent of Quarter Horses carry this gene. It’s most common in cutting horse bloodlines, where its prevalence is as high as 28 percent.

Polysaccharide Storage Myopathy (PSSM)
A horse with this disease has unregulated synthesis of glycogen, the storage form of sugars, in his body. This causes him to store too much glycogen in his muscles, which then leads to stiff, painful muscles and episodes of “tying up” (whole-body muscle cramping).

How is it inherited? Like HYPP, PSSM is a dominant gene, with incomplete dominance. Your horse is likely to be severely affected if he’s homozygous (carries two genes for the trait), and less severely affected if he is heterozygous (carries only one gene for the trait). And if he’s homozygous for PSSM, all of his offspring will have the disease—but its severity will depend on which gene they inherit from their dam. If he’s heterozygous, he’ll only pass on the gene to 50 percent of his offspring.

How common is it? It’s estimated that approximately 10 percent of Quarter Horses carry this gene. In the halter horse bloodlines, its prevalence is 28 percent.

[READ ABOUT: Muscle Maladies]

Glycogen Branching Enzyme Deficiency (GBED)
A horse with this disease lacks the enzymes needed to store glycogen. Without stored glycogen, the brain, heart, and muscles are unable to function. This disease is always fatal. Affected foals are most commonly aborted or stillborn. If born alive, they’re unlikely to survive for longer than a couple of weeks.

How is it inherited? This disease is autosomal recessive, meaning that only homozygous recessive individuals are affected. Just like HERDA, if your horse is heterozygous (has only one copy of the gene) he’ll be a carrier, meaning he won’t show any symptoms at all, but can still pass the gene off to his offspring.

How common is it? Estimates say that eight to 11 percent of Quarter Horses are carriers, and up to 26 percent of horses with Western pleasure bloodlines carry the gene.

Malignant Hyperthermia (MH)

This disease causes a disruption of the channels, or pathways, that control the release of calcium in your horse’s muscles. Affected horses have an excessive release of calcium that leads to a “hypermetabolic state” during periods of stress, such as extreme exercise or when undergoing anesthesia. During an episode, your horse’s heart will race, he’ll sweat, and his temperature can rise to as high as 109 degrees. A severe episode can easily be life-threatening.

How is it inherited? This disease is autosomal dominant with complete dominance, meaning your horse will be equally affected whether he’s homozygous (has two genes) or heterozygous (has only one gene). This pattern of inheritance reduces the chance that unidentified carriers will be responsible for further spread of the disease—although you might never know your horse is affected if he doesn’t experience an episode.

How common is it? The incidence of MH is not yet known.

What Does It All Mean?
The five-panel genetic test helps you not only manage your horse’s individual health, but also make informed breeding decisions that might help reduce the incidence of these diseases. Unfortunately, some of the best performing horses are also carriers of these diseases—and breeding strategies like line-breeding (used to help concentrate desirable traits) also causes these genetic diseases to become more prevalent.

So what decision should you make if you learn that your horse carries one of these genetic diseases? The answer may not be as simple as it seems.

If you’re a purist, with a purely scientific way of thinking, the answer may seem obvious—if your horse carries one of these diseases, don’t breed him. If the carriers are never bred, the disease could be eradicated within a generation.

But what if that carrier also happens to be perfect in every other way? He’s sound, strong, has a super temperament, and is a world-class performer. Aren’t those traits worth preserving? That is the horseman’s dilemma—and why the answer isn’t always black or white.

The middle ground says genetic testing allows breeders to identify what horses are carriers to make smart decisions. Is he an average horse but carries a genetic disease? Don’t breed him. Is he a superstar that’s heterozygous for a recessive disease like HERDA or GBED? Don’t breed him to another carrier, and you can rest assured your foal won’t be affected. (Although it could still be a carrier.) Over time, careful breeding is likely to help gradually reduce the prevalence of the disease, while preserving positive traits.

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