A look at the new genetic testing tool that could save studs and owners a lot of money

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Here, Martin Stevens speaks to Equinome’s chief science officer Professor Emmeline Hill about Checkmate – subscribers can get more great insight every Monday to Friday.

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The latest genetic testing tool launched by Equinome could save thoroughbred studs and racehorse owners considerable amounts of money.

Checkmate does what it says on the tin: checks potential matings, in this case for the risk of genomic inbreeding, as high levels have been linked to mid to late-term pregnancy loss and lower racing durability in the resultant foal.

Equinome claims that it is the first mating tool in the world that enables breeders to reduce the risk of foal loss before a final breeding decision is made.

Genomic inbreeding is the amount of double copy DNA in an individual and cannot be gleaned from the position of duplicated ancestors in a pedigree. Horses can be significantly more or less inbred than might appear from that information.

Inbreeding to notable ancestors has long been seen as a method of repeating desirable characteristics in a foal, but the thoroughbred population has become so closely related that doing so increases the odds of doubling up on negative traits.

Recently published research led by the Royal Veterinary College in Britain shows an association between higher genomic inbreeding levels and abortions and stillbirths, which should make breeders sit up and take notice, as foals lost late in gestation can harm the mare’s health and reduce the farm’s revenue.

High levels of genomic inbreeding have also been shown to significantly impact a foal’s durability for racing. Published studies led by University College Dublin and Equinome show a clear link between genomic inbreeding and the likelihood of a thoroughbred horse ever racing. 

Good Morning Bloodstock was given a sneak preview of Checkmate by Equinome’s chief science officer Professor Emmeline Hill.

“A mare owner sends in a blood sample from their mare, and using that we generate a DNA profile for her that the breeder can then match to stallions contained within our database,” she explained.

“There is a page that gives an initial overview, showing the five stallions most genetically similar to the breeder’s mare and the five most genetically different from her. There is also a diagram that illustrates the mare with all the stallions on the database plotted around her in relation to their genetic similarity.

“For every mare a breeder can choose up to ten different stallions to check her against, the idea being that they will have already drawn up a shortlist based on other factors they’ll take into consideration. Think of it as a final health check, like a pre-purchase exam but for breeding.”

The results of the potential matings are given a Checkmate Genomic Inbreeding Prediction score that is either very high (which Equinome recommends avoiding based on evidence from those published scientific papers), high (should be carefully considered), average (should be considered) and low or very low (both fine to proceed with as there is a lower or significantly lower risk).

Hill continued: “We have also conducted a case study of 1,000 matings across 28 stallions on multiple farms in the Weatherbys Return of Mares for 2019 and 2020, where we had DNA profiles for the sire and the mare. 

Professor Hill: "Think of it as a final health check, like a pre-purchase exam but for breeding"Credit: Peter Houlihan / Fennell Photography

“We used Checkmate to predict genomic inbreeding level for each mating and found that the lower predicted inbreeding for the book of mares highly correlated to an increase in the number of live foals per stallion.

“The most striking finding was that when the average Checkmate Inbreeding Prediction in the book of mares was high, it produced 59 per cent live foals, whereas if it was low, the rate of live foal production rose to 76 per cent.

“There aren’t so many cases of slipped foals reported in the Return of Mares, but again we found that matings with a very high Genomic Inbreeding Prediction were 5.2 times more likely to result in a slipped foal.

“Those figures show that this tool is as valuable to stallion owners as much as mare owners, or even more so, as it could save fortunes in lost fee revenue.”

A test run on Checkmate produced a fascinating result. Hill selected a daughter of Gone West on her own version of the program and chose at random several potential stallions, and invited me to do the same. 

I picked Iffraaj, a paternal grandson of Gone West, to see whether the mating would create a very high Genomic Inbreeding Prediction. It did; but so too did one of the randomly selected stallions who shares no ancestors with the Gone West mare within four generations. It goes to show that duplications on a tabulated pedigree, or the absence of them in this case, aren't a reliable indicator of how much identical genetic material might actually be inherited.

Checkmate features around 400 stallions, including 26 of the top 30 in Europe at present. Even when Equinome hasn’t had blood samples submitted by studs, it can usually produce a DNA profile for them.

“If we have a sufficient number of progeny of a stallion, we can generate a DNA profile for him that is 99.9 per cent accurate,” says Hill.

“Using the speed gene test as an example, if you’ve got a large number of foals by a single sire who are all either CT or TT you know the sire can’t be CC or CT, he must be TT, and you can do that across all genetic markers; tens of thousands of them. It’s a process geneticists call inferring.”

Not every stallion master is a fan of genetic testing and so the Checkmate database will lack a few new sires in their ownership, which is a shame as the program makes no qualitative judgements on the ability of a horse: it merely highlights the risk of genomic inbreeding when mated with different mares. 

Those naysayers are potentially shooting themselves in the foot as Checkmate could increase the number of foals successfully born, and therefore fee income, and also boost the rate of racecourse starters, if the breeder takes the decision to reduce the risk of genomic inbreeding.

There are also plenty of pedigree enthusiasts who will likely be surprised to hear inbreeding spoken about in negative terms when Enable, one of the best horses of modern times, is by Nathaniel, a paternal grandson of Sadler’s Wells, and out of Concentric, a daughter of Sadler’s Wells. Surely it can’t be that bad, then, they might be justified in thinking.

Enable (right): by Nathaniel, a paternal grandson of Sadler’s Wells, and out of Concentric, a daughter of Sadler’s WellsCredit: Getty Images

“That breeding probably increases the chance of her being genomically inbred but it is unlikely it contributes to her being elite; it’s far more likely that she’s inherited elite gene variants,” says Hill. “Studies have found no link between genomic inbreeding and elite performance.

“Assuming she is genomically inbred, which we can't say for sure, she will have effectively beaten the odds by being born healthy and making it to the track.

“We do see in the live population a huge variation in levels of inbreeding, with some who are very highly inbred. What inbreeding does is increase the chance of double copy, but it doesn’t say exactly where in the genome that is. 

“What you are doing by inbreeding is increasing the chances of doubling up on recessive mutations that might impact on the biological fitness and viability of a foal during pregnancy. We haven’t yet got to the point that we can identify the genes that have the harmful mutations, but what we can do for now is reduce the chance of them occurring.”

The price of Checkmate is €200 or £175 per mare for one year’s access. It isn’t bad value, in the context of thoroughbred breeding, especially if seen as any other supplement that contributes towards the birth of a healthy foal.

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