Discovering another genetic disease in the Quarter Horse

Research behind a recessive genetic disease found in Quarter Horses was recently published by researchers at the University of California-Davis. Equine Juvenile Spinocerebellar Ataxia (EJSCA) causes ataxia, or loss of coordination, of foals carrying two copies of the gene, and is always fatal. Individuals carrying only one copy of the gene are not affected. Breeding carriers has a 25% chance of producing a foal with no EJSCA, a 50% chance of a foal with one copy of the gene, and a 25% chance of a homozygous EJSCA foal.  

Foals inheriting two copies of EJSCA start to show mild incoordination in their hind limbs around 10 days after birth. The progression of the disease is rapid, with fore limbs and other parts of the neurological system quickly degenerating to the point that the foal is not able to stand and requires euthanization. 

Lynda McCall 

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Dr. Jim and Lynda McCall have been involved with raising and breeding horses for more years than Lynda can count.  

Jim graduated from Texas A & M with a Ph.D. Physiology of Equine Reproduction in 1972, and developed the A & M horse program as a graduate student. Dr. McCall went on to develop the horse programs at the University of Maryland and Louisiana Tech University, creating courses in equine behavior, management, reproduction, nutrition and training.  

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After Jim left the academic world over 30 years ago, the couple started breeding cutting horses at their home near Mount Holly, Arkansas. Continuing to share their experience, McCalls wrote for major equine publications such as the Quarter Horse Journal and co-authored and published books on horse training and reproduction. 

Although Jim is now past 80 and in poor health, they still have a few foals every year. After a lifetime involved with horses, “You think you’ve seen everything,” Lynda said.  

A few years ago, two of their mares foaled within a few days of each other. 

“About day 10, one baby got where all of a sudden she was struggling to get up,” Lynda said.  

“‘What the heck is going on?'” she wondered. After a visit from their vet, Dr. Ron Nash, Lynda spent several days helping the filly get to her feet. 

“I would go out and tail her up every three or four hours to let her drink,” she said.  

But every day the filly grew worse, and it got to the point that Lynda didn’t have the strength to help her keep her balance while she nursed. 

“She just kept degenerating. One at a time she lost control of different parts of her body. She didn’t ever lose her sucking response, and I remember her sitting on the ground, propping herself up, and her mama would come put her bag right above her mouth so she could reach up and suck.”  

At some point during the first foal’s ordeal, the second mare foaled. 

“It was born normal, running around like little foals do. We had the two mares in foaling stalls at different ends of the barn, so it wasn’t something they could catch.” 

The first foal degenerated to the point she couldn’t stand at all, and they had to euthanize her. The first foal was “barely cold,” Lynda said, when the second foal started showing the same symptoms. 

“It was almost on the hour, to the day,” she said. “The sequence was really fresh in my mind, and dammit if that second baby didn’t go through the whole damn deal again.” 

It was déjà vu all over again. 

Lynda called Dr. Nash and told him something was going on, and she thought they needed to get some DNA. They had already taken the first foal to their “animal cemetery” area, but she and Dr. Nash went down to salvage what they could of tissue samples, even though the coyotes had already done their work. 

They also gathered DNA samples from the two mares and the foals’ sire, and Dr. Nash sent it all to Texas A & M. 

The second foal went through the same sequence of symptoms, following exactly the same timeframe. 

“You just couldn’t believe what you were seeing,” McCall said.  

This time, having to put the foal down was not a surprise. 

“I hate putting down foals,” McCall said. “I remember sitting on the ground with it, and saying to Dr. Nash, ‘I feel like I’ve been God-smacked.'”  

If this had happened to one foal, McCalls would have assumed that it was a freak accident, that somehow it got injured. 

“With two babies simultaneously going through the same thing, almost to the hour and minute, we knew something was going on,” she said. 

When Dr. Nash followed up on the samples they had sent to Texas A & M, he learned that they had been sent on to U.C. Davis. 

“Dr. Nash was very involved and communicated a great deal with Dr. Finno,” Lynda said. “He called me and said, ‘you’re not going to believe this. They have had six other cases.'” 

Lynda called Dr. Finno at U.C. Davis to learn more, particularly about the bloodlines of the other affected foals. Due to confidentiality practices, the research team was not able to share much information with her. At that point, Dr. Finno was not certain that they were dealing with a genetic disorder, but was investigating these cases.  

“It just bugged the hell out of me,” McCall said. “I couldn’t sleep at night. I think I talked to her on a Friday and Monday I called back. ‘I can’t even imagine the odds that this would happen to two horses almost simultaneously, to the day, to the hour, almost to the minute of the expression of the progress of the disease, if it wasn’t genetic,’ I told her.” 

Lynda hesitated to breed the two mares back the same way, as they figured whatever caused the foals’ issues had to be a recessive gene. 

Jim said to go ahead and breed them. “We’ve only got a 25% chance we’ll get another one,” he told Lynda. 

While she knew this was true, waiting and watching after the two mares foaled the following spring was excruciating.  

“Day one. Day two. Day three. Day four. Day five. Day six. Day seven. Day eight. Day nine. Day 10. Nothing happened, and both mares were bred back to the same stud. We bred them back again the following year and those foals were also normal. That one quirky thing set this whole thing off.” 

McCall believes knowing about the EJSCA genetic variant is valuable for Quarter Horse breeders. 

“I don’t think it will have the frequency of HERDA,” she said. “It was certainly hard to catch since it is a recessive gene.” 

McCall reiterated that EJSCA is most likely not a new mutation, and eliminating all carriers would not serve the Quarter Horse breed well. 

“How long has it been in there? Hundreds of years?” she asked. “For that gene to be in there, it has to do something in the body that is positive, otherwise if it was an extreme negative response in the body it would have wiped itself out of the herd. There are all sorts of complexities; it ain’t that simple, folks.” 

Laura Teague 

Laura Teague also went through the harrowing loss of a foal to EJSCA.  

April born foal became severely ataxic around 10 days of age, and initially Teague assumed it was due to an unknown injury. 

“We brought them to a stall in the barn and started trying to figure out what was going on,” she recalled. “We had her X-rayed, and thought we saw some vertebral changes. We had a chiropractor treat her and she improved for a little bit, but she became laterally recumbent on one side. Eventually she got depressed and wouldn’t eat any more. She had a tremendous mom, but when the foal couldn’t stand on her own we had to stay up all night and feed her every two hours.” 

At the end of her rope, Teague finally had to make the decision to euthanize the filly.  

In the meantime, Teague had posted on Facebook about the foal, and Brenda Armstrong, owner of PG Heavily Armed reached out to her, saying that she had seen a couple of foals like that on her farm, and that it sounded like the same thing. 

“Neither one of us had any idea this disease existed at that point,” Teague said.  

In May, Teague heard about the EJSCA research recently published by U. C. Davis. She immediately started researching the disease and sent off a DNA sample to get Taggline tested. 

“I had a pretty strong feeling that the foal we lost was affected,” she said. 

Sure enough, Taggline’s test revealed that he was a carrier of EJSCA. Teague immediately posted an announcement on Facebook for their clients’ information.  

“I got the mare tested, called Brenda and she got her mares tested; we all kind of deduced that this was what our foals had,” she said.  

By now, Teague had already bred her mare back to Taggline. She conferred with Dr. Finno at U.C. Davis about the situation. 

“She didn’t think terminating the pregnancy was the smart thing to do,” Teague said. “When this foal is born we can send hair in for a STAT test to find out if it is affected or not.” 

Teague is aware of two or three more mares in foal to Taggline that could be carriers and could possibly produce a homozygous EJSCA foal. 

“They are not my own mares, but the owners have a protocol in place to send hair off and get the foals tested immediately when they are born,” she said. 

Teague has reached out to two AQHA board members, requesting action to get the EJSCA test on the required disease panel test as soon as possible.  

“I am frustrated,” she said. “They said it is not a big enough issue to act on immediately, and will wait until their March 24 stallion rules board meeting and decide then if it is important enough to put it in the genetic disease panel. This infuriates me; I have a couple of carrier mares and am looking for non-carrier stallions. I can make a decision as a mare owner to not breed to a stallion if he is a carrier, but why not make it a required test? It is so devastating and costly for foals to be born and have to be euthanized because of this.” 

Teague is frustrated that AQHA is not making EJSCA testing a bigger priority. 

“There is not enough awareness of this disease,” she said. “A large percentage of owners who lose a foal to it will just assume that there was an accident. Losing this foal was so heartbreaking. When we found out what she must have had, it was a relief.” 

Teague intends to be very up front with mare owners who want to breed to Taggline. She intends to require any mare with Freckles Playboy in her pedigree to be tested negative for EJSCA before breeding. 

“There is responsibility on the mare side too, but some people are not aware that EJSCA exists,” she said. “I will probably do some research on the pedigrees of mares before we breed. I’m pretty open and transparent and really believe I have a great stud; part of the reason he’s great is his bloodlines. They are great too.” 

Although it’s been a challenging situation, Teague believes that having the test available for EJSCA is important. 

“It’s really good for the industry to know about it,” she said.  

Dr. Carrie Finno 

In March of 2020, U.C. Davis School of Veterinary Medicine Finno Laboratory, of which Dr. Carrie Finno is the Principle Investigator, was contacted about the first case of what is now known as EJSCA. 

“The veterinarian had suspected equine neuroaxonal dystrophy (eNAD) after all tests came back negative for known neurologic diseases,” Dr. Finno said. “The foal became unable to stand and was euthanized. At necropsy, it was apparent that the foal did not have eNAD.” 

Dr. Finno and her team were subsequently contacted by veterinarians in Texas about additional cases and discovered that all of these foals were related individuals.  

“The evidence supported that this was a new, heritable disease,” she said.  

One of the most difficult questions to answer as the U.C. Davis team worked through the research was where (i.e. in what gene) the suspected mutation was located.  

“With the addition of more affected foals and their relatives to our study in 2021-2023, as well as the inclusion of large whole genome databases of different horse breeds, we were able to narrow down a significant genetic region of interest for deeper analysis, which is where we found the mutation we suspect is associated with EJSCA,” Dr. Finno said. “The fact that all the cases were related, as well as the shared similarity of all clinical signs, was a strong indicator that EJSCA is an inherited disease.”  

Dr. Finno’s pedigree investigation continues to support the hypothesis that this is an autosomal recessive disease.  

“Additionally, we have genotyped all known cases, carriers, and Quarter Horse and non-Quarter Horse controls for the suspected mutation, which has resulted in the perfect segregation of the mutated allele. Cases all have two ‘affected’ copies, carriers all have one ‘affected’ copy, and controls all have zero ‘affected’ copies,” she said. 

The U.C. Davis research team does not have an exact estimation yet on the prevalence of EJSCA in the Quarter Horse breed.  

“Research in this area is ongoing,” she said. “We expect the allele frequency to likely be significantly higher in some Quarter Horse sub-disciplines compared to others, similar to other inherited diseases.” Currently, Dr. Finno’s graduate student, Ms. Briana Brown, is investigating the allele frequency of EJSCA across Quarter Horse sub-disciplines, in collaboration with the UC Davis Veterinary Genetics Laboratory.  

It is important for Quarter Horse breeders to know that this is an autosomal recessive disease, so carriers bred to carriers have a 25% chance of producing an affected foal. Dr. Finno believes that EJSCA should be added to the required panel test for AQHA breeding stallions. 

“The disease is severe, rapidly progressive, and fatal. We would advise breeders to continue following best breeding practices. If they have reason to believe their stock may be a carrier for EJSCA, it is advised to have them tested,” she said. “The severe and fatal nature of this disease indicates that this should be added to the AQHA panel test to prevent additional foals being born with EJSCA.” 

There is currently a test available at the UC Davis Veterinary Genetics Lab for this disease, accessible through their website:  https://vgl.ucdavis.edu/test/equine-juvenile-spinocerebellar-ataxia-ejsca 

As foaling and breeding seasons approach, owners, breeders and veterinarians should watch for indications of EJSCA. 

“Based on all the cases we have seen so far, affected foals experience an acute onset of signs one to five weeks from birth,” Dr. Finno said. “These foals show impaired coordination in the hind limbs, followed by the forelimbs, and will have a difficult time turning to either side without stumbling. Typically, within a week or less, these signs quickly progress to the inability to stand without assistance. Affected foals do not recover with supportive care.”