MATP — cream and pearl

What it does

Crossing two of them

Its gene carrot

Gene key

horsegenetics.matp

Alleles

Cr prl sun sno N

Combinations

15

Outcomes

5, plus two carrier wild types

Default allele

N

Priority

40

Founder draws

1 × nextFloat()

Deterministic

yes

Four dilutions at one locus

SLC45A2 carries four known dilution alleles, and they are alleles of the same gene — which is the single most consequential fact about it, because it means they compete for the two slots a horse has and can compound with each other.

The combination table

This is the table no single word describes. Cr on its own is a partial dilution; prl on its own is nothing; two prl is a different dilution again; and one of each is stronger than either. “Incomplete dominant” was never going to say that, which is why there is no dominance property any more — the rows below are the whole model.

The eye follows the same rows

A double dilute's pale blue eye is the famous one, and it is not the blue of a splashed white horse: the iris has all its pigment cells, they are simply not handling enough melanin to colour it. So it claims at RANK_DILUTION, the lowest of the three routes, and loses to the depigmented blue rather than competing with it.

This locus does not paint an iris. It requests an allele at the two iris loci, and the allele is written onto the horse at birth — so a cremello genuinely carries LBl/LBl, shows the pale blue, and passes it on to foals that are not cremellos.

Deterministic, like the coat: every cremello has the same pale blue eye, so this locus costs the coat cache one entry per outcome and not one per horse. The full account of the channel, the ranks and heterochromia is on Eye colour & heterochromia.

The numbers

Red is always restricted more than black under a double dilution, which is why a diluted bay body fades to cream while the points hold smoky colour. Each outcome also carries a black tint (see PigmentField.dilute) so the points land in a real diluted-black hue instead of the gradient’s jet-black zero-red column.

Founder frequency

Allele frequencies 1/30 for Cr and 1/22 for prl — the same numbers the two old genes carried, so the wild population is unchanged apart from the impossible genotypes disappearing. The gene declares the resulting six shares directly rather than computing them, so an author can retune one row without touching the others:

FounderTable.builder()
        .weight(Cr,  Cr,  0.111111)
        .weight(Cr,  prl, 0.303030)
        .weight(Cr,  N,   6.141414)
        .weight(prl, prl, 0.206612)
        .weight(prl, N,   8.374656)
        .weight(N,   N,  84.863177)
        .build();

One gene, four dilution alleles

MATP — now usually called SLC45A2 — is a pigmentation gene and nothing else. The locus is multiallelic: a horse has two copies, and each may be normal N, Cream, Pearl, Sunshine, Snowdrop, or something not yet found. Cream and Pearl are not separate genes, and neither are the two newer ones.

So “palomino”, “buckskin”, “cremello”, “perlino” and “pearl” are phenotype labels arising from combinations of this locus with a base colour — not names of single genes. Which is exactly the structure the mod implements: five alleles at one locus, and outcomes read off the pair.

Cream, which is the one with a dosage effect

One Cr most visibly dilutes pheomelanin. A buckskin keeps dark mane, tail, legs and ear edges because those are eumelanin — and the reason is not that cream “fails” on black pigment, but that at one dose its visual effect on eumelanin is much less obvious than on red. Smoky black can be so subtle that it passes for an ordinary dark, sun-faded or seal-brown horse without a test.

Two copies dilute both pigments far more. Double-cream horses characteristically have pale pink or rosy skin and pale blue eyes, and are frequently miscalled “white” — they are dilute-coloured horses, not genetically white-patterned ones. Their pale hair is hair with reduced pigment, not an absence of pigment cells the way most white spotting works. Perlino often keeps a warmer, peachier cast in mane, tail and lower legs; smoky cream can read warmer or darker than a typical cremello from residual pigment. UC Davis, cream

Pearl, and the compound heterozygote that fools everyone

Pearl is autosomal recessive: N/prl is an outwardly non-pearl carrier, prl/prl shows the dilution, and Cr/prl shows a strong dilution because the horse has no normal allele at the locus at all. It is also called apricot, and historically the Barlink Factor in Quarter Horse colour discussions.

Homozygous pearl gives a diluted body, mane and tail with pale skin; on chestnut, a relatively uniform pale apricot. On bay and black backgrounds the outcome varies more, because base colour and unidentified modifiers change how much residual dark pigment shows.

Cr/prl is the famous one: very pale coat, pale or pinkish skin, blue or blue-green eyes — a pseudo-double-dilute that may be impossible to distinguish from cremello, perlino or smoky cream without DNA testing, despite carrying only one cream allele. UC Davis, pearl

Sunshine and Snowdrop

Both are newer, rarer, and much thinner on evidence than Cream and Pearl. Both behave primarily as recessive dilutions: a carrier looks non-dilute, and two dilution alleles at the locus can give a strongly pale, double-dilute-like phenotype.

Sunshine

Reported in 2019 after investigation of a horse that looked like a double-cream dilute but tested as carrying only one cream allele. Glycine 190 becomes arginine — small and flexible replaced by large and positively charged, plausibly disruptive, though that is an inference from the substitution rather than a demonstrated mechanism. The allele is named C^sun after Captain Sunshine, the horse in which it was recognised; he was pale cream in coat, mane and tail with blue eyes, and was Cr/sun, not Cr/Cr. The study also found the allele heterozygous in one non-dilute offspring, supporting a single copy being visually silent. Anim. Genet. 10.1111/age.12790

The biggest gap is sun/sun. There is no robust body of documented homozygotes defining the chestnut, bay or black phenotype, typical skin and eye colour, residual point pigment, or whether expression is as consistent as prl/prl or Cr/Cr. A 2026 breed-colour report described a second Cr/sun horse, a Tennessee Walking Horse colt from a carrier dam — useful evidence the allele is not confined to one family, and an emerging observation rather than a population study.

Snowdrop

Reported in 2020 in a Gypsy horse with a very dilute coat that carried none of the then-known explanations. Arginine 102 becomes glutamine; the allele is C^sno. The reported sno/sno horse showed strong dilution of both red and black pigment and looked like a homozygous cream. In the discovery pedigree, both sire and dam carried one copy with no observable effect. bioRxiv 851246

Snowdrop is the clearest evidence that this locus should be understood as a series of functional dilution alleles rather than a two-allele normal-versus-cream system. Cr/sno, prl/sno and sun/sno are all uncharacterised in published evidence. It is tempting to assume any two non-normal alleles here give a strong phenotype — a reasonable hypothesis given the Cream/Pearl and Cream/Sunshine observations, and not a settled fact.

Cream is the odd one out because one copy shows. The other three are best treated as recessive or recessive-like functional alleles: a normal allele preserves enough SLC45A2 activity that the carrier is not visibly diluted, while two altered copies substantially reduce pigmentation.

Skin and eyes

Skin is dose- and genotype-dependent: single-cream horses usually keep dark skin under coloured areas, with pink skin under ordinary white markings; double-cream horses commonly have pink or rosy skin; homozygous pearl shows paler skin; and Cr/prl commonly has pale or pinkish skin. Pink skin is not disease and does not mean a lethal-white foal — it means little visible melanin at that location.

Eyes. A single cream allele generally has little obvious effect. Double-cream horses commonly have blue eyes; Cr/prl can have blue or blue-green; pearl homozygotes may have lighter eyes, less uniformly described. A light eye alone cannot diagnose the genotype — blue eyes also come from several white-pattern genes, notably splashed white. The mod handles that collision the same way, by ranking the eye contributions rather than letting the last one win.

Health

Current references treat cream and pearl as coat-colour dilutions, not disease mutations. The breed-distribution study notes that some pigment variants do have medically important pleiotropic effects — and names silver/MCOA, frame overo/lethal white, and leopard complex/CSNB as the examples. It identifies no comparable association for cream or pearl.

So: no established lethal effect, no developmental disorder, no proven eye malformation association, no CSNB association, and no adverse syndrome tied to Cr/Cr, prl/prl or Cr/prl. The same holds for sunshine and snowdrop, with the caveat that being very rare and recently recognised is not the same as having every subtle effect excluded.

“Dilution” is a visual category, not a biological or health one. The one real management point is that pale skin has less natural UV screening — shade, UV fly masks, sun sheets — which follows from pigmentation generally and is not a disease phenotype of these alleles.

Build, size, jumping, speed

None are known to be caused by any allele at this locus. No credible evidence links cream or pearl to withers height, bone circumference, head shape, muscling, frame, body mass, growth rate, adult size, hoof quality or structural soundness; nor to jumping scope, technique, carefulness, bascule, tendon durability, trainability or competition results; nor to sprint speed, race performance, stride length, aerobic capacity, fibre profile, recovery or gaitedness. The best-known single-gene association with alternate gaits is DMRT3.

Where colour looks associated with performance in a real population, the candidates are breed structure (cream is common in some populations and absent from others, and breeds differ enormously in what they were selected for), founder effects (a notable stallion carrying both a colour allele and athletic traits), breeder selection for colour and type together, and plain visual bias — pale horses can look larger or finer-boned depending on light and contrast.

Breeds and frequency

Cream is widespread. In the UC Davis dataset of 11,281 horses across 28 breeds it was detected in 25 of the 28. In the relatedness-filtered sample its frequency ran from 0.42 in Lusitanos down to 0.013 in Standardbreds, and it was not detected in the sampled Hanoverian, Knabstrupper or Percheron groups — absent from those samples, not proven absent from those breeds. PMC9498372

Pearl is much more restricted, with a strong Iberian distribution consistent with where it was first identified. It appeared in 7 of the 28 breeds:

Those are allele frequencies, not percentages of visibly pearl horses — and since pearl needs prl/prl or Cr/prl to be conspicuous, visible pearls are far rarer than carriers. The tiny Quarter Horse figure fits the historical Barlink Factor label: it exists and is uncommon. The 11–12% in Iberians makes pearl a live breeding consideration there.

Sunshine and Snowdrop have no population frequency at all. Sunshine was first identified in a horse of Standardbred × Tennessee Walking Horse ancestry, with a later Tennessee Walking Horse colt and carrier dam — enough to make that ancestry worth testing, and not enough to say the allele “belongs” to either breed. No peer-reviewed survey has established a frequency, an origin breed, a founder, a geographic distribution, or whether it is genuinely rare or merely rarely tested. Snowdrop is known in Gypsy horse / Cob / Tinker ancestry, with laboratory guidance noting that presence elsewhere has not been described and cannot be excluded. “Rare” is a fair description and not a measured percentage.

What is settled, and what is not

Strongly established. Cream and pearl are alleles of SLC45A2/MATP; cream is c.457G>A / p.Asp153Asn; pearl is c.985G>A / p.Ala329Thr; cream acts with a dosage-dependent, incomplete-dominance pattern; pearl is recessive alone and interacts visibly with cream in compound heterozygotes; both affect coat, skin and eye pigment; and there is no established direct effect on athletic ability, conformation or size.

Still uncertain. The full molecular mechanism — SLC45A2 clearly participates in melanosome pigmentation, and the exact chain from each equine variant to each visual phenotype is unresolved. Why horses with the same colour genotype vary in shade, mane and tail colour, residual point pigment and eye tone. Which additional genes govern shade, seasonal change and flaxen-like mane effects. Whether very subtle physiological effects of altered pigmentation exist below the threshold of detection — there is no evidence for any, so none should be assumed. And essentially everything about sun/sun and the snowdrop compounds.

The practical caution, and it is the one this locus exists to teach: visual colour names cannot replace genotype here. A pale blue-eyed horse can be Cr/Cr, Cr/prl, Cr/sun, sno/sno, or something at a different locus entirely.