Genome Sequencing in Horses and Solutions for Genetic Disorders

In 1995, 70 scientists from around the world gathered in Lexington, Kentucky, to make plans for an ambitious goal. Spurred by the human genome project – the plan to map the entire human genome – these scientists hoped to do the same thing for the horse genome.

Because of financial and technological limitations in 1995, however, “it was inconceivable that we’d ever have a genome sequence,” said Dr. Ernest Bailey, a genetic researcher at the Gluck Equine Research Centre in Kentucky. Over the next 12 years though, the group continued to meet and collaborate and, by January 2007, they had mapped and sequenced the entire horse genome.

Today, more than 200 horses have had their genomes sequenced – a process that goes further than mapping. While mapping identifies major landmarks in the genome, sequencing identifies the order of every part of the DNA. This data has pushed the boundaries of equine research.

Scroll to continue with content

Initially, the researchers believed that once they knew the sequence of a horse’s genes, most of the secrets of heredity would be unlocked because they could translate what they knew about the human genome to the horse genome. What they found, however, was that 98 per cent of the horse genome does not contain genes. This large majority of the horse genome is made up of what scientists used to call “junk DNA” or noncoding DNA. At first glance, this DNA appeared to serve no biological function. With further research, however, scientists are discovering that some of this DNA does have a function, although most of what it does remains a mystery.

Dr. Bailey worked on the original Horse Genome Project and continues to collect data and examine the ways genes can influence horse health and performance. While there have been some exciting discoveries, Dr. Bailey warns that “we still don’t know a lot about the horse genome. The next step forward is going to be an improvement on how we can analyze the data.”

Genetic research is a little bit like a treasure hunt, as researchers continue to uncover the function of certain genes and how they impact the horse. Here, we break down for you what genes are, why you should care about them and some of the exciting research that’s happening right now in Canada and around the world thanks, in part, to the knowledge gleaned from the Horse Genome Project.

Genetics 101

Before delving into how genes influence horse breeding, health and performance, it’s important to have a basic understanding of what genes and DNA are and how they function. And so we start at the beginning, when a foal is first conceived.

Chromosomes, which are located within the nucleus of cells, carry hereditary material from the stallion and mare to the foal. Each animal has two copies of each chromosome – one from its mother and one from its father. Horses have 32 pairs of chromosomes for a total of 64 chromosomes. Each chromosome is made of a single double-stranded molecule of deoxyribonucleic acid (DNA) and other proteins.

So where do genes factor into all of this? A gene is the segment of the DNA molecule that carries the ‘instructions’ to produce proteins that build the cells of a horse. Each horse has two copies of each gene, one on the chromosome from its mother and one on the chromosome from its father. Different forms of the same gene, called alleles, produce genetic variation in traits ranging from coat colour to height.

The genes a horse carries for a certain trait, such as a distinctive marking like a star, are referred to as the genotype. The product of the genotype – the star that you see on a horse’s face – is called the phenotype.

The different alleles for any given gene may act in a dominant/recessive, co-dominant or semi-dominant manner. If a horse has matching alleles for a trait, they are called “homozygous” for that trait. If they have different alleles for a trait, they are “heterozygous” for that trait. In coat colour, for example, the bay allele is dominant to the black allele. In order for a horse to be black, his parents must both pass on their black alleles to him, thus the horse would be homozygous black. The horse, however, will be bay if even one parent passes on a bay allele. Thus a bay horse could be either heterozygous or homozygous for the bay allele.

You have probably heard the term ‘genetic mutation’ used to describe irregularities like dwarfism in the horse population. But a mutation doesn’t necessarily have to be bad. In fact, evolution relies on mutations to create genetic diversity. If, for example, a mutation like ‘easy keeping’ proves advantageous to a horse in a place where grazing is scarce, that horse would thrive and produce more offspring, thus passing on this mutation to future generations. This is probably one of the reasons wild ponies thrive in barren areas.

A mutation can also occur to a horse’s genes during its lifetime – even while it is still in the womb – due to an error in DNA replication during cell division. These errors can be caused by environmental factors as well. Further adding to the confusion are diseases that at first glance can appear the same as some genetic disorders, but actually aren’t genetic disorders. These are called phenocopies.

A good indicator that a disorder is genetic is if it is prevalent in a particular breed. The reason for this is obvious – horses of the same breed typically share the same genetic heritage. In the world of genetic disorders, cross-bred horses escape largely unscathed because their genetic background is more diverse.

“Since most of the disorders we see are recessive, they are less likely to be seen in cross-bred horses where only one of the parental breeds is carrying the mutation,” said Dr. Dianne Winkelman-Sim, who has a Ph.D. in genetics and is an equine science lecturer at the University of Saskatchewan.

Single Gene Disorders

When people think of genetic disorders in horses, they are most likely thinking of single gene disorders like hyperkalemic periodic paralysis (HYPP) – a muscle disorder in Quarter Horses – or severe combined immunodeficiency in Arabian horses – a disorder where the foal is born with an undeveloped immune system, rendering him defenseless against opportunistic infections.

As noted above, single gene disorders usually impact horses of the same breed because the horses that are bred together share the same genetics. Today, thanks in part to the sequencing of the horse genome, there are tests for many of these disorders. Breed registries will sometimes even go as far as implementing rules that bar horses carrying markers for certain disorders from registration or breeding programs. One example of this is the American Quarter Horse Association’s decision, in 2004, to bar from registration foals born in 2007 or after who are homozygous for the HYPP gene. The intention of rules like this is to “lessen the genetic load’ – a term that refers to the number of genetic disorders a certain species carries.

“I feel that we do have an ethical responsibility to work towards eliminating the genes that cause genetic disorders,” said Dr. Winkelman-Sim. She qualified her statement, however, by noting that people shouldn’t just stop breeding any horse that carries an identified mutation known to cause a genetic disorder. “There are a number of factors that need to be taken into consideration and it is not practical to attempt to remove all genetic disorders from the population.

Some things to consider are how widespread the genetic disorder is in a population, the severity of the disease and if the gene that causes the disorder may also be linked to traits that are considered desirable in a horse.

An example of a single gene disorder that fits this category is congenital stationary night blindness (CSNB), which is found in Appaloosas. Horses with this condition are unable to see in the dark because of a genetic mutation on the TRPM1 gene that is also linked to a specific type of Appaloosa coat patterning. This mutation is called leopard complex, or LP, and horses who are homozygous carriers suffer from CSNB. The phenotype of this disorder is the blocked white areas on the horse’s coat.

Dr. Lynne Sandmeyer, a professor of veterinary ophthalmology at the Western College of Veterinary Medicine (WCVM) and a researcher investigating CSNB, said, however, that other genetics can become involved that mask the phenotype and the only true way to determine if a horse suffers from CSNB is to do a genetic test or an ophthalmologic exam.

According to Dr. Sandmeyer, the mapping and sequencing of the horse genome fast-tracked the research of the geneticists who were working to identify the exact gene that caused CSNB. In 2008, the researchers identified the TRPM1 gene using a candidate gene study – a technique where researchers use prior knowledge of a gene’s function. Or, to put this technique in simpler terms: “You know that the gene does something in one species, so you sequence it and see what happens in another,” explained Dr. Bailey.

Although researchers now know what gene causes CSNB in Appaloosas, it is one of those disorders that cannot simply be eliminated from the population through selective breeding because the disorder is also linked to one of the qualities that “make the Appaloosa the Appaloosa,” said Dr. Sandmeyer. “My understanding, from talking to breeders, is that the horses that are homozygous for LP arevaluable breeding animals. They produce those beautiful leopard spotted horses,” she said.

Dr. Sandmeyer said the true value in identifying the horses with CSNB is that owners are now able to understand what limitations the condition can put on an animal. “If you know that a horse can’t see in the dark, you’re obviously going to be careful around that animal in the dark and take certain precautions when it’s night time,” she said. “These horses have been around thousands of years and we’ve only recently discovered how common this disorder is in the breed, so they have been adapting.”

That hasn’t stopped Dr. Sandmeyer from trying to develop a treatment to correct this condition though. Currently, she is working on a gene therapy in mice that also don’t have a functioning TRPN1 gene, but it’s in the initial stages of development. The treatment involves injecting the gene into the back of the eye using a viral vector – a virus that has all the infectious components taken out of it and now carries helpful material to correct a condition. “It certainly is a huge undertaking to start using it in the horse and research-wise we’re probably still a few years away,” she said of the possible treatment.

Dr. Sandmeyer added that another benefit of continuing CSNB research in horses is that they can potentially serve as an animal model for humans that have similar types of night blindness.

For many other single gene disorders, however, gene therapies might not be a practical application because it runs counter to the goal of most breeders – which is to breed the most robust animal possible. “If you start looking at gene therapy and fixing errors that are wrong in the animal, then you can continue to breed them and increase the genetic load on a population,” said Dr. Winkelman-Sim. “So, I don’t think (gene therapy) is a really practical route to go in terms of what you would do with horses.”

Using Genetic Knowledge to Fight Common Disorders and Diseases

Identifying single gene disorders is perhaps the simplest example of how applying the knowledge gleaned from the horse genome project has benefited equine research. However, there are many other more complex ways that researchers can and have used knowledge of the horse genome to gain insights into other common disorders.

At the University of Montreal, Dr. Jean-Pierre Lavoie has been working on getting a better handle on what causes heaves in horses by identifying genetic markers associated with persistent inflammation in a horse’s lungs. “Heaves is a very common disease in horses in Canada,’ he said. ‘The best estimate we have is around 15 per cent of adult horses seven years of age or older are affected in Canada and western Europe.”

Dr. Lavoie said the mapping and sequencing of the horse genome was a “major breakthrough,” because it accelerates the process through which his research team can identify genes that are expressed when a horse’s lungs are inflamed by heaves or inflammatory airway disease (IAD).

“We need to study proteins and other molecules that may be dysregulated in the disease process,” said Dr. Lavoie. “The first step is often to look at the gene expression, which is the message that will be sent to the cell machinery that will lead to the synthesis of proteins and other molecules.”

Some of his research looks at how and when IAD (a disease characterized by coughing and exercise intolerance) turns into full-blown heaves and what might be predictors for this. “We’re trying to identify simple diagnostic means to diagnose heaves that would allow us to go back into younger horses – horses with IAD – and say, well, this horse is predisposed to heaves,” he said.

Dr. Lavoie said that one day, when definite markers linked to heaves are identified, veterinarians may be able to use a blood test to identify the young horses who suffer from IAD who are most at risk for it developing into heaves. The benefit of this would be that owners could take preventative measures – such as stabling a horse away from allergens – to reduce the risk of the horse developing heaves.

As for a genetic test that would tell breeders what breeding stock could pass their heaves genes onto their offspring, that day is quite far off in Dr. Lavoie’s opinion. “I don’t think genetic tests will be the answer in the near future because of the complexity,” he said. “In humans, they’ve spent millions and tens of millions on this and they’re still not close to finding a gene pattern that allows them to identify predisposed patients.”

Unlike in a single gene disorder, in a condition like heaves, the relationship to the genetic predisposition is not straightforward. A horse’s genetics may predispose them to heaves, but a complex interaction with the environment will ultimately determine if the horse has a mild form of IAD or develops heaves.

“We don’t have a really good handle on [the genetic basis of complex diseases] at this point,” said Dr. Bailey. “What we are doing now is looking at heaves, parrot mouth, developmental bone diseases and other issues and we’re using research tools to look for single genes that have a big effect. We know that a single gene doesn’t cause these problems, but we are hoping we can find genes that have a major effect. If we can, then maybe we can find a treatment to reduce the severity of some of these issues.”

Exciting Applications

The equine genome treasure hunt has yielded some interesting findings for breeders. Much of it is kept secret, however, and commercialized for profits according to Dr. Bailey. He pointed to a company based in Dublin, Ireland, that has proprietary rights on a genetic test that can predict the best race distance for a horse.

The company was founded by Dr. Emmeline Hill, who with her team, discovered that variants of the MSTN gene (which encodes for the protein myostatin, whose main function is to control the growth of muscles in the body) could predict what particular distance a racehorse would perform best at. The alleles for this trait are marked either as the letter C or T. Since each horse has two alleles for each gene that are inherited by the sire and dam, each racehorse can have one of three possible genetic combinations for the different speed traits: C:C, C:T or T:T. Therefore, each racehorse can have one of three possible genetic combinations for the different speed traits: C:C, C:T or T:T.

C:C horses are the sprinters of the horse world. They are early maturing, well-muscled horses that earn on average four times more prize money than a T:T horse. Their best distance is 1,000 to 1,600 metres.

C:T horses are the middle of the pack racehorses, with a mixture of speed and stamina, they are the most versatile runners. They are best suited to distances of 1,400 to 2,400 metres.

T:T horses are best suited to distances that are longer than one mile and require stamina. They are later maturing and normally don’t perform well as two year olds. However, as three year olds they have been known to win big races like the Oaks and the Melbourne Cup.

Dr. Bailey said this type of genetic research is competitive. ‘It’s commercial and so a lot of it hasn’t been published and there are at least four or five companies worldwide that do genetic testing for Thoroughbred breeders and advise them which horses may not be good performers and they may want to avoid purchasing,’ he said.

But even with all of this knowledge about the ‘speed gene,’ it is still impossible for breeders to predict what horse will be a champion. In fact, there is a disclaimer – in bold – on the Equinome website that says: This test is not designed to identify how good a horse is likely to be, but rather what it will be good at.

‘The experiment I’d like to see are the horses who were champions at sprinting, didn’t have this particular allele and ask what are the other genes that they have that are making them good sprinters, despite not having this gene,’ said Dr. Bailey, who noted that for certain traits researchers have identified genes for there may be other as-yet unidentified genetic components that produce the same effect – it’s all part of the dearth of information in horse genetics. ‘That is one of the difficulties we have in genetics. We look at a trait and say, ‘Oh, here’s a trait, let’s look at what the genetics of it are.” But while researchers may think they’ve identified a genetic marker for a certain trait, a candidate gene study may fail to produce a genetically visible commonality in a group of horses that share the trait in question. Dr. Bailey uses his recent study of parrot mouth as an example:

‘We had a group of 30 horses with parrot mouth and we tested them for certain markers, and we compared them to normal horses, but we were disappointed because we didn’t get any strong hits [for the culprit gene],’ he said. ‘The problem could be that there may be three different [genetic] ways to produce a parrot mouth and if we put all three of them in the same group it’s going to confound our ability to make a discovery.’

So, not only do researchers need to have an equine genome map and sequence, they must also ask the right questions in order to make discoveries in the genetic arena. In some sense, it seems almost as though the mapping and sequencing of the equine genome has brought forth more questions than it has answered.

It was Socrates who said, ‘The only true wisdom is in knowing you know nothing,’ and this quote seems particularly apt when talking about equine genetics.

That’s not to say the mapped genome isn’t a magnificent tool, but it is still just one tool in the world of horse breeding, performance and management. Good management, proper conditioning and training must still come into play to ensure the best health and performance from our horses. With a better understanding of genetics, the horses we start with may be healthier or better suited to a certain discipline, but there are still several factors that remain beyond our understanding and control. ‘Basically, the horse we start with should be better; the product we end up with will still be no better than what we make it,’ said Dr. Winkelman-Sim.

COMMON SINGLE GENE DISORDERS

HYPP: Hyperkalemic periodic paralysis is a hereditary muscle disorder that most commonly affects Quarter Horses, but can also affect breeds with Quarter Horse bloodlines, like Paints and Appaloosas.

First identified in the 1980s, the disorder can be traced to a single Quarter Horse sire named Impressive, a champion halter stallion who died in 1995. The disorder affects the sodium channels in muscle cells, which leads to uncontrollable muscle twitching and weakness. HYPP is unusual for a single gene disorder as it is a dominant trait, meaning even a heterozygous HYPP positive horse has a 50 per cent chance of producing offspring with HYPP. However, a horse that is heterozygous for HYPP will not be as severely affected by the disorder as a horse that is homozygous for the trait. It can be treated through diet and medication. The AQHA can provide a genetic test for the disease for $40. Foals homozygous for
HYPP are no longer permitted in the AQHA registry.

HERDA: Hereditary Equine Regional Dermal Asthenia or Hyperelastosis Cutis (HC) is a recessive disorder characterized by fragile skin that easily sloughs off, creating open wounds, typically on the back of the horse, but also the legs.

Quarter Horses are usually affected, but any horse carrying Quarter Horse bloodlines can suffer from the disorder. The disorder can be traced back to the stallion Poco Bueno and the AQHA provides a genetic test for this disorder as well. HERDA-like symptoms have also been observed in other breeds – notably a Swiss Warmblood filly that German researchers found did not have the same gene mutation that HERDA affected Quarter Horses had. Therefore, a different mutation is most likely at play in other breeds. There is no known cure and affected horses are usually euthanized because their wounds fail to heal properly.

SCID: Severe Combined Immunodeficiency is a recessive genetic disease that was identified in Arabian horses in the early 1970s. Affected foals are born without a properly functioning immune system and within months after birth succumb to opportunistic infections like pneumonia. Since 1997, a genetic test has been available for this disease, so breeders can avoid breeding two parents who carry the recessive trait. Interestingly, horses that carry the marker for SCID are more susceptible to sarcoids (skin cancer). About eight per cent of the Arabian horse population carries the mutation for this disease.

Equine Dwarfism: Equine dwarfism is typically seen in miniature horses, however, a certain type of dwarfism has been known to affect Friesian horses as well. Dwarfism is a recessive trait, but as of yet there are no genetic tests to identify the genetic mutation that produces dwarf traits. As such, sufferers can only be identified through phenotypic expression. Some traits include twisted legs, contracted tendons and extremely short limbs, domed head, protruding jaw and bulging eyes. Dwarfism is estimated to be in 60 per cent of the miniature horse population and there is considerable debate within the community about the ethics of breeding certain traits that some may find aesthetically pleasing, but may cause health problems in the animal.

JEB: Junctional Epidermolysis Bullosa or hairless foal syndrome or red foot disease is a disorder found in Belgian Draft horses and other draft breeds. A related disorder, JEB2 occurs in American Saddlebreds. Foals born with the disorder show no immediate symptoms. Within days, however, they develop skin lesions, lose their hoof walls and develop oral ulcers. These foals are also usually born with front teeth. The disorder is caused by a mutation that inhibits the production of a protein that is responsible for holding skin onto the body. These foals are usually euthanized within days for humane reasons. There are genetic tests available for both JEB1 and JEB2.