DNA colour testing in horses
Which loci are tested, how to pull hair with the roots, which laboratory to send it to, what it costs and why pearl is tested before any breeding.
The colour in the passport is written by an inspector. He looks at the horse and picks a word off a list. That is phenotype — what was visible on one particular day, in one particular light, at one particular stage of the coat change. The genotype is written by a laboratory, and it never changes.
For buying a horse to ride, the difference often does not matter. For breeding it decides everything: what goes into the foal is genes, not colour.
Why the eye cannot be trusted
My stallion's dam, CASIA PM, is recorded in the studbook as chestnut. She is a pearl carrier. Nothing about her shows it — not the body, not the eye, not the skin. One copy of pearl does not express, and any inspector would write exactly what is written there.
The same mistakes happen with other genes:
- grey cannot be read at a year to eighteen months, the horse is recorded bay and turns white by ten;
- a foal in its birth coat can be lighter or darker than the adult colour;
- a sun-bleached black drifts into brown;
- under grey nothing underneath is visible at all.
A test answers the question the eye cannot settle: what the horse will pass on.
What a locus is and what gets tested
A locus is the place in the genome where a particular gene sits. Laboratories sell either single loci or a ready-made panel.
| Locus | What it shows |
|---|---|
| Extension (E) | base pigment: black or red |
| Agouti (A) | distributes black — black or bay |
| Cream (Cr) | cream: palomino, buckskin, the cremellos |
| Pearl (prl) | pearl, the hidden one |
| Dun (D) | dun with dorsal stripe and leg barring |
| Grey (G) | whether the horse greys, and how fast |
| Champagne (Ch) | champagne dilution |
| Silver (Z) | silver dapple on black and bay |
| KIT (Tobiano, Roan, Sabino, White) | tobiano, roan, white patterning |
| Leopard complex (LP) | blanket and leopard patterns |
| Splashed white, Frame overo | white patterns, one of them tied to health |
The baseline for any horse is Extension and Agouti: they explain what the main pigment is doing at all. After that you add by breed. For the PRE, pearl, cream and grey are worth having. Tobiano and leopard do not occur in the breed, and there is no reason to pay for them.
Worth remembering separately: some of the white-pattern tests are veterinary genetics rather than aesthetics. Frame overo in a double dose is lethal to the foal. That is the case where the test is not about colour.
Taking the sample
Blood is rarely used. The standard is hair with the roots attached.
- Pull, do not cut. A cut hair is useless: the DNA is in the follicle, not the shaft.
- Take from the mane or the tail, right at the root, in small strands of five to seven hairs.
- You need 20 to 40 hairs with visible white bulbs. Count them against the light.
- The horse has to be dry and clean. A wet mane after washing means mould in the envelope.
- Put the sample in a paper envelope, not a plastic bag. Seal it, write the name and the UELN on it.
- Do not handle samples from two horses on the same table.
A foal can be tested from day one. Birth-coat tail hair works, but the follicles are smaller, so take extra.
Where to send it, how long, how much
There are not many laboratories with an international reputation. In the United States it is the Veterinary Genetics Laboratory at UC Davis, Animal Genetics in Florida, and Etalon Diagnostics in California. In Europe the usual addresses are Laboklin in Germany, Genomia in the Czech Republic, Animal Genetics' UK arm, and the laboratories accredited to the breed associations. Spanish PRE breeders normally go through a laboratory recognised by ANCCE, because that result is accepted by the studbook.
Order of magnitude from the published price lists: a single locus runs about $25–45 or 25–45 €, a six-to-ten locus panel $90–200 or 90–200 €, and the wide all-in panels that Etalon sells go past $300. The exact figure comes only from the laboratory's own page on the day you order, because price lists get revised. Turnaround is 5 to 20 working days from receipt of the sample, plus post.
The report arrives by email as a PDF with the genotype at every locus tested. That is the document you show a buyer. The colour description in the passport is not a document.
Why pearl is tested on its own
Pearl is recessive. A carrier with one copy cannot be told from an ordinary chestnut or bay horse — not from a photograph, not in person, not under a lamp. Genes do not add up into a warning: they sit there and wait for a second carrier.
Two consequences for breeding follow.
First. If you are buying a mare to put under a pearl stallion, the pearl test is done before the sale, not after. The whole arithmetic hangs on the result: with a carrier mare half the foals come out double pearl, with an ordinary mare they all come out carriers and look like nothing in particular.
Second. If a double pearl has appeared in your line, both sides were carriers, and the other offspring of those parents are open questions too. They need testing.
How pearl differs from cream, and why it gets called cremello, I covered separately. The whole picture of the diluting genes is here, and the full list of colours with the terminology is in this article.
What the test gave me
Godo PM is recorded in the LG PRE ANCCE studbook as bay double pearl: bay base, two copies of pearl. Homozygous. That is not an assessment by eye, it is a genotype from a laboratory.
The practical meaning of that one line in the report: there is no third option for him, and every foal gets pearl — not half, all of them. What happens after that depends on the mare, and that is her test, not his.
His sire, SOL PM II, is also a double pearl. His dam, CASIA PM, is a carrier. Which is why Godo's colour was not a surprise at foaling but the breeder's calculation.
What I say plainly: a test confirms genetics and nothing more. It promises nothing about movement, height or temperament. Colour is the first thing people look at, and the horse has to be lived with for the rest of its life.
If you are working out a pearl breeding, the colour grid and the semen terms are on the breeding page. Bring your own test result and we will calculate your mare rather than an abstract one.
