Checkmate: An inbreeding test to help with foal viability

Cover image courtesy of The Image Is Everything

Equinome is a world leader in equine genetics research, and their Speed Gene Test has a 90 per cent accuracy in determining the best distance for a racehorse. Owned by Zinto Labs, an animal genetics research company, Equinome continues to push into the science of Thoroughbred genetics.

The Speed Gene test

“We launched our first DNA test in 2010. The speed gene test was the first time anyone in the world had identified a gene connected to a particular trait in Thoroughbreds. It’s highly predictive of best race distance and we found that a single gene has a massive influence on one trait,” said Donal Ryan.

The basic speed gene test gives the user three outcomes for their horse:

C:C Sprint/Mile Types

C:T Middle Distance Types

T:T Staying Types

“Since then the technology has developed rapidly, and now we have a suite of tests which are more complex. They look at a wide range of genes determining health and performance. We also provide genomic research in a range of other species, which are mostly racing species, as well as some conservation and companion animals.

“We have a team with a set of capabilities that we can apply primary research to other species, identify certain traits, then turn that into a commercial test with online delivery of results to customers.

“Australia has always been strong supporters of our Speed Gene Test. We’ve noticed that across all our clients, Australians are very open to innovation. We also see that in the move towards sport science by trainers in Australia and the way trainers have embraced out enhanced speed gene test with our additional more complex testing.

“Trainers such as Lindsay Park, Ciaron Maher, Danny O’Brien and others, all use this to identify quickly what distance will suit a horse. It’s given them the best chance to react quickly with a horse. Often the DNA tests will match the physical and pedigree, but it does throw up some surprises.”

The Speed Gene Test looks at the Myostatin gene which is responsible for the regulation of muscle development. This gene has featured in multiple published studies by Equinome researchers and others, and has shown race-distance aptitude can be determined from this gene with 90 per cent accuracy.

Checkmate and what it offers

“The Thoroughbred is our heritage at Equinome. We have deep connections to the industry, and we are trying to push what is possible genetically. The ultimate goal is to understand what the challenges are in the industry and how we can help solve them. We see Checkmate as a key tool in a broader tool kit for breeders.”

Checkmate looks at a broodmare’s DNA profile and checks it against a breeder’s ten preferred stallions to determine the level of inbreeding in the potential foal.

“We have developed a platform to check the mating’s inbreeding level, so before you make a final decision, you can look at the predicted level of inbreeding. This isn’t about pedigrees, it’s at the DNA level. A pedigree can tell you the likelihood of inbreeding, while DNA tells you the actual.”

Inbreeding and why is it a problem?

It’s been known in the scientific community that high levels of inbreeding in a population leads to inbreeding depression and a higher likelihood of recessive genes being seen in the phenotype of the individual. Two key terms here are genotype – the genetic structure of an individual – and phenotype – what an individual looks like. Another term that is useful is epigenetics, which is basically how the genotype changes as a reaction to the environment.

In humans, 70 per cent of our brain development happens after being born, so nurture has a big impact on how well someone reaches their genetic potential. Horses are born more mature relative to humans, but the way they are grown and their environment also makes a difference to reaching that genetic potential.

But inbreeding depression begins before the nature vs nurture argument. The problems with high levels of inbreeding in a population were first recognised by Charles Darwin in 1876. The famed Hapsburg family who ruled Germany, Austria, and Spain were a stark example of the impacts of high levels of inbreeding with the ‘Hapsburg Jaw’ caused by the family’s tendency to marry their cousins to keep power in the family. After two centuries of rule, the family all had a sharply jutting jaws, bulbous lower lips, long noses, and most importantly hugely decreased fertility until the line failed to produce any heirs.

The genetic level understanding of what was happening with inbreeding depression began in the late 1990s when scientists were looking at populations of endangered species and how zoos could resurrect and expand populations without encountering the issues associated with inbreeding depression.

“Our recent test leans into that. Basically, Checkmate determines the level of inbreeding in an individual. Inbreeding has become a focal point recently with concerns about high levels of inbreeding resulting in reduced health of the breed, from foals through to individual mares, and lower soundness of racehorses.

“Several studies on the level of inbreeding and its affects have been done by the likes of the US Jockey Club, University of NSW, University of Edinburgh, Cornell University and the Royal Veterinary College in England, and they’ve all found that the level of inbreeding (in the Thoroughbred) has accelerated in the last 25 years as stallion book sizes have increased. It’s not necessarily a surprise, but now we have scientific evidence.”

The impacts of inbreeding depression

The currently accepted definition for inbreeding depression is “the reduced survival and fertility of offspring of related individuals.” In racehorses, the higher levels of inbreeding recently come from higher book sizes for stallions. Ironically these bigger books are possible thanks to improvements in broodmare veterinary work. Stallions aren’t doing any more work than they used to do, but better veterinary work has meant that stallions now only need to cover a mare once to get her in foal, rather than four or five times as they did when Northern Dancer (Can) was at stud.

“The Royal Veterinary College’s research correlated higher inbreeding in foals to mid to late term pregnancy loss.” The study, published in March 2024, was led by Dr Jessica Lawson, Alborada Trust Research Fellow at the RVC, and Professor de Mestre at the Baker Institute for Animal Health at Cornell University, together with previous PhD student at the RVC, Dr Charlotte Shilton, analysed DNA samples from 189 individuals and found Thoroughbred pregnancies lost in mid and late gestation had significantly higher inbreeding than across the whole Thoroughbred population, while pregnancies lost early in gestation showed a range of level of inbreeding.

“An increased level of inbreeding has also been looked at in several other studies, some that (Equinome) did, and others in Australia and the Northern Hemisphere, and all of them correlated higher levels of inbreeding to poor racing durability. The studies weren’t consistent (in inputs) but they are comparable. In Australia, the studies looked at the likelihood of getting to the races, while the American ones looked at the length of career, however they all showed the same outcome. As inbreeding rapidly increased there was a correlation to unsoundness.”

Essentially all these studies are pointing to one thing. A higher level of inbreeding in Thoroughbreds is leading to less fitness across the breed and this is seen with late term pregnancy loss and a reduced soundness when racing.

“Historically inbreeding (in thoroughbreds) has been done for positive traits, but more recently the higher levels of homozygosity have been having negative effects.”

Checkmate’s outcomes for your breeding stock and income

“The idea is to better understand what’s good and what’s negative by looking at DNA. Checkmate will allow a mare can be checked against 10 sires, with an outcome range from high coefficient of inbreeding to low.”

Checkmate is designed so a breeder can still make all the decisions about which stallion will suit a mare based on the usual things - type, performance, commerciality, and pedigree – and then will provide a ‘health check’ to determine if any of those matings are higher risk for pregnancy loss.

“Since we established Checkmate, we’ve looked retrospectively at the matings done in Ireland and England and this has been a group of over 1000 mares. We looked at the outcomes of those matings, and the stallions with the highest average levels of inbreeding in their foals had 59 per cent live foals, while those with the lowest levels of average inbreeding among their resulting matings went up to 76 per cent live foals.

“It’s quite stark and powerful when you see these results, especially for stallion owners where no foal equals no fee. Basically, higher inbreeding in foals results in a loss of income for stallion owners because they’ll end up with a lower number of live foals. The reverse is proven to be true too. Matings with a lower average inbreeding figure results in more live foals, so higher stallion incomes.

“And not only are more foals getting born, they are also more durable, more likely to race and this potentially has a longer-term impact on a stallion’s career.”

How can customers access Checkmate?

“We have a digital platform so customers can log in, create a profile, and then send mare samples to us. We sequence them, then the results are visible to the client. From there, a client can match their mares against the couple of hundred sires we have in our system. It’s $330 for 10 matches, and for each one, you can see predicted level of inbreeding for each mating."

For those worried that this will be Northern Hemisphere focused, given that Equinome is a Northern Hemisphere based business, Ryan said, “We have a strong representation of Australian stallions. (Checkmate)’s launch is a little bit late for this season, but we have had good response from Australian breeders to join in for next season.

“It’s important to note that this isn’t about performance. It’s more of a veterinary health check to avoid high risk matings and ensure a live foal. It gives stallion owners a significant return on investment with an increase in live foals. The big owner-breeders are looking to utilise this to its full capacity.

“One of our clients made the point that it’s not about trying to produce a Group 1 winner. It’s about avoiding a bad horse. We aren’t competing with pedigree analysts or mating plan specialists. This is a scientifically verified way to avoid negative health risks via genetic identification.”

“We’ve tried to price (Checkmate) at the level of a veterinary checkup to keep it affordable for our clients too. The consequence and impact of a slipped foal is much more expensive. Anecdotally we are hearing from the big vet clinics that there’s an increase in hereditary issues that they haven’t seen before compared to 15 years ago, and we know that the level of inbreeding has been increasing in that time too.

“We are maintaining our focus on ‘how does this help the customer?’ It’s key for us to make this science ‘actionable’ where it helps produce healthier, sounder horses, and avoid high risk matings that result in pregnancy loss.”