The test two pony breeds wrote into the licence

Until 2010 there was a foal that Fell pony breeders had learnt to dread without being able to name what was wrong with it. It was born looking like any other, nursed, stood, and then at two to four weeks began to fade — pale gums, a cough or a runny nose that would not clear, infections that did not answer to treatment — and was dead or put down before it was three months old. The researchers who eventually found the cause put the loss at roughly one Fell foal in ten each year. The Dales, a closely related breed with a shared history in the northern dales, started seeing the same thing in 2009. Nobody could prevent it because nobody could see it coming: the parents were healthy, the foal was healthy, and then it was not.

What the test found

The condition is Foal Immunodeficiency Syndrome, and it is a lethal recessive. A foal has to inherit the faulty gene from both parents to be affected; a pony with one copy is a carrier, perfectly healthy, and indistinguishable from a clear pony by any means other than a laboratory test. A team at the Animal Health Trust and the University of Liverpool, led by Dr June Swinburne, pinpointed the gene at the end of 2009 and published the full account in 2011: a single missense change in SLC5A3, a transporter gene, on equine chromosome 26. A hair-sample carrier test went on sale on 1 February 2010 for forty pounds. In its first month the Trust received 119 samples.

The numbers that came back were the shock. Screening in 2009 and 2010 found that roughly forty per cent of adult UK Fell ponies and twenty per cent of adult Dales ponies were carriers. Mate two Fell ponies at random and the odds of an affected foal were roughly one in twenty-five; mate two carriers and they were one in four. That is not a rare-disease statistic. It is a breed in which the faulty allele had become, quietly, one of the most common things about it.

The decision that mattered

What the two societies did next is the reason this piece exists. The Fell Pony Society had already said, in the spring the test launched, that it would test every colt or stallion licensed for the first time that year. That has since hardened into rule: it is compulsory for a colt or stallion to be FIS tested before a stallion licence can be issued, and the licence is only granted once the DNA parentage result and the FIS result are both in and the passport and records updated. The Dales Pony Society went one step further. Since 2012 every colt must test clear, not merely tested, to be eligible for licensing; the Society holds hair samples for every registered pony, every colt is microchipped and DNA profiled, and the FIS certificate must be in the Secretary's office before a licence application is even considered. The Society's own words are as plain as a rule can be: it will not license carrier colts.

Set that beside the piece we wrote on what a stallion's licence actually proves. A licence, we said, is a veterinary floor a stallion must clear before his foals count as fully registered. What the Fell and Dales societies did was to bolt a genetic floor onto the veterinary one. A Dales colt can pass the vet, match his sire on the DNA test, and still be refused because of a single letter in SLC5A3 — and his progeny, if anyone uses him anyway, go to Section X of the stud book, from which there is no upgrading. That is a society using the one lever it has that individual breeders do not.

Why the mares were left alone

There is a temptation, reading this, to ask why the same rule was not applied to mares, and the answer is the most instructive part of the story. Both societies explicitly allow carrier mares to breed, on the condition that the stallion is clear. The Dales page puts it as a question and answer: should I avoid breeding from my carrier pony? No — but you must ensure that any stallion you use is clear. The lab that sells the test says the same thing more directly, that carriers should be retained for breeding to preserve diversity.

The arithmetic behind that is the one we set out in why rare breeds don't breed the carriers out. If two in five Fell ponies carry the allele, removing every carrier from breeding removes two in five of the breed, and with it a share of everything else those ponies carry that is worth keeping. A 2013 paper from Professor Stuart Carter at Liverpool, which the Fell Pony Society quotes on its own health page, reported that only one foal tested positive in 2012 — the disease, in other words, had been all but stopped within three seasons — while noting that the strategy of allowing carriers to breed with clears would not reduce the large number of carriers. The societies chose that trade deliberately. They stopped the foals dying, which was the thing that could be stopped quickly, and accepted that the allele itself would fade only as slowly as a small breed can afford. For breeds on the Rare Breeds Survival Trust's watchlist — the Dales is in the Priority category on the 2026/27 list, the Fell is At Risk — that is the right order to do things in, and the reasoning is the one we laid out in what an effective population size actually tells you: the scarcer the breeding stock, the more expensive every exclusion becomes.

The New Forest, and the sample in the tube

The New Forest Pony Breeding and Cattle Society faced a different disease and made a similar choice, and its experience adds the caution the Fell and Dales story would otherwise lack. In the summer of 2017 the Society was notified of a New Forest pony carrying PSSM1, a muscle disorder that is dominant rather than recessive — there are no carriers, a horse has it or does not — and began testing every New Forest stallion at its own expense immediately. From 2018 every colt coming forward for inspection has been tested at the Society's cost and licensed only if clear. The mantra on the Society's page is one any breed could adopt: to prevent affected foals, test before you breed.

Then, in February 2026, the Society published an update that took some courage to write. Woodfidley Top Gun, a forest-run stallion licensed in 2009 and dead since 2023, had been reported clear in 2018. A retest in 2026, using hairs from the original 2018 sample and DNA-matched back to his 2009 profile, came back positive. He is now listed among the lines known to carry the condition; the Society is offering free testing of his progeny born since 2018, voluntary rather than mandatory, and positives keep their breeding status with the stud book record corrected. Nothing about the scheme's design was wrong. A result was wrong, and the only reason anyone knows is that the Society kept the sample, kept the profile, and was willing to go back and look.

What this tells a buyer, and what it tells us

For someone buying a Fell or Dales pony, the practical upshot is simple. A licensed stallion of either breed has been FIS tested as a condition of that licence, and for a Dales stallion the result is clear by definition. A mare may be a carrier, and that is fine, provided you know it and provided the stallion is not. The result is recorded on a certificate the society can verify; the Fell Pony Society would like owners to have it written into the passport too, and after the first tampered certificate turned up in 2024 it is worth asking for the lab report rather than a photocopy. That sits inside the wider point we made in what a horse passport actually proves: the passport establishes who the pony is, and the certificate establishes something about what it carries, and neither is much use without the other.

For a marketplace, the lesson is the one we keep arriving at from different directions. The Fell and Dales societies did not need a new technology to nearly eliminate a lethal disease in three years. They needed a forty-pound test that already existed, and the will to make it a condition rather than a recommendation. A listing that shows the result, names the laboratory, and links back to the society that holds the sample is not adding anything to that achievement. It is just making sure the work they did is visible at the moment a buyer is deciding whether to trust it.

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Sources

• Health — The Fell Pony Society
• Registration and licensing fees — The Fell Pony Society
• FIS — Dales Pony Society
• Colts and stallions — Dales Pony Society
• Fox-Clipsham et al., "Identification of a mutation associated with fatal Foal Immunodeficiency Syndrome in the Fell and Dales pony", PLoS Genetics, 2011
• Fell Pony Society offers genetic tests for new stallions — Horse & Hound, March 2010
• PSSM — New Forest Pony Breeding & Cattle Society
• PSSM1 update, February 2026 — New Forest Pony Breeding & Cattle Society
• Watchlist 2026–27 — Rare Breeds Survival Trust

— Rene