Horse Coat Color Calculator

Comparison chart of horse coat colors showing bay, chestnut, black, palomino, buckskin, and cremello phenotypes — Figure 1. The six most common horse coat colours produced by combinations of the Extension (MC1R), Agouti (ASIP), and Cream (SLC45A2) gene loci. Bay and black share the same Extension genotype (E_) but differ at Agouti. Palomino and cremello share the same Extension genotype (ee) but differ in Cream gene copy number.

The Three Primary Genes That Determine Horse Coat Colour

Horse coat colour is a classic example of epistasis — where one gene masks or modifies the expression of another. The three primary loci work in a strict hierarchy: Extension sets the base pigment capacity, Agouti controls its distribution (but only if Extension allows black pigment), and Cream dilutes the resulting colour.

1. Extension Locus — MC1R Gene (Chromosome 3)

The Extension locus encodes the melanocortin 1 receptor (MC1R), a G-protein-coupled receptor on melanocyte surfaces. When activated by alpha-MSH, MC1R triggers the switch from pheomelanin (red/yellow) to eumelanin (black/brown) synthesis. Horses with at least one dominant E allele (EE or Ee) produce functional MC1R and can make black pigment throughout the body. Horses homozygous recessive (ee) have non-functional MC1R — they can only produce pheomelanin and are therefore chestnut.

Homozygous dominant. Always passes E. All offspring can produce black pigment.

Heterozygous. Passes E or e with equal probability. Phenotypically non-chestnut.

Homozygous recessive. Chestnut base. Can only pass e. No black pigment possible.

2. Agouti Locus — ASIP Gene (Chromosome 22)

The Agouti locus encodes the agouti signalling protein (ASIP), an antagonist of MC1R. ASIP competes with alpha-MSH for MC1R binding. Where ASIP is active, it inhibits eumelanin synthesis and promotes pheomelanin production. In bay horses (A_), ASIP expression is restricted to specific body areas — the points (mane, tail, lower legs) — leaving the body reddish-brown. In black horses (aa), loss-of-function mutations in ASIP mean the inhibitor is absent, allowing uniform eumelanin deposition. The Agouti locus only has a visible effect when the horse can produce black pigment (E_ genotype) — it is completely epistatic to Extension in chestnut horses.

Homozygous dominant. Bay. Always passes A — no black offspring possible.

Heterozygous. Bay phenotype but carries black allele. Can produce black offspring.

Homozygous recessive. Black. ASIP non-functional — eumelanin throughout.

3. Cream Gene — SLC45A2 / MATP Gene (Chromosome 21)

The Cream gene (a variant in the SLC45A2 gene, also historically called MATP) is an incomplete dominant dilution gene. It reduces pigment density in both eumelanin and pheomelanin pathways, but affects pheomelanin more strongly. One Cream copy (nCr, heterozygous) dilutes chestnut to palomino and bay to buckskin. Two Cream copies (CrCr, homozygous) produce a much stronger dilution: chestnut becomes cremello (pale cream body, blue eyes, pink skin), bay becomes perlino (cream body with slightly darker mane and tail), and black becomes smoky cream. The Animal Genetics equine cream gene reference provides molecular detail on the SLC45A2 variant responsible.

nN — No Cream

No dilution. Base coat colour fully expressed.

nCr — 1 Copy

Single dilution. Palomino (chestnut) or Buckskin (bay).

CrCr — 2 Copies

Double dilution. Cremello (chestnut) or Perlino (bay).

How Extension, Agouti, and Cream Combine — Full Coat Colour Reference

The final coat colour depends on which alleles are present at all three loci simultaneously. Extension acts as the master switch. Agouti is only relevant in E_ horses. Cream modifies the resulting base colour.

Extension	Agouti	Cream	Coat Colour
E_	A_ (bay base)	None (nN)	Bay
E_	aa (black base)	None (nN)	Black
ee	Any (irrelevant)	None (nN)	Chestnut
E_	A_ (bay base)	1 copy (nCr)	Buckskin
E_	aa (black base)	1 copy (nCr)	Smoky Black
ee	Any	1 copy (nCr)	Palomino
E_	A_ (bay base)	2 copies (CrCr)	Perlino
E_	aa (black base)	2 copies (CrCr)	Smoky Cream
ee	Any	2 copies (CrCr)	Cremello

Worked Horse Colour Genetics Examples

Example 1 — Two Palomino Parents

Palominos are genotype ee (chestnut base) + nCr (one Cream gene). Breeding two palominos produces offspring across three colours in the Cream locus — a classic incomplete dominance cross for the Cream gene.

Parent 1: Palomino (ee + nCr)

Parent 2: Palomino (ee + nCr)

25% Chestnut (ee + nN)

50% Palomino (ee + nCr)

25% Cremello (ee + CrCr)

Ratio: 1 : 2 : 1

The Cream gene behaves as an incomplete dominant — one copy produces palomino, two copies produce cremello. This cross follows the same 1:2:1 pattern as any heterozygote × heterozygote cross, identical to incomplete dominance in snapdragon flowers.

Example 2 — Two Bay Heterozygotes: Bay × Bay

Bay horses that are heterozygous at both Extension (Ee) and Agouti (Aa) can produce four different coat colours, including black foals — despite both parents appearing bay.

Parent 1: Bay (Ee + Aa)

Parent 2: Bay (Ee + Aa)

~56% Bay (E_ + A_)

~19% Chestnut (ee + any)

~19% Black (E_ + aa)

~6% Other combinations

Example 3 — Can Two Chestnut Horses Produce a Bay Foal?

No. Chestnut is the recessive base colour at the Extension locus. Both parents are ee genotype and can only pass on e alleles. Every offspring is ee — chestnut. Agouti and Cream genes are irrelevant because no black pigment can be produced.

Chestnut × Chestnut = Always Chestnut

This is the most reliable rule in horse colour genetics. A foal claiming to be bay from two registered chestnut parents indicates either a recording error or non-parentage.

Other Horse Coat Colour Genes Not Modelled Here

Beyond Extension, Agouti, and Cream, numerous additional genes modify horse coat colour. Each follows its own inheritance pattern, and some involve dominant white mutations with potential homozygous lethal effects.

Grey (STX17)

Progressive greying with age. One dominant Grey allele causes gradual depigmentation of the coat. All grey horses will eventually go white regardless of base colour. Dominant — a single copy is sufficient.

Dun (TBX3)

Produces a distinctive dilution with a dorsal stripe, leg barring, and sometimes a shoulder stripe ("primitive markings"). Dun dilutes black pigment to mouse-grey and red pigment to yellow.

Roan (KIT region)

Causes an even mixture of white and coloured hairs throughout the coat. Heterozygous roan horses maintain coloured head and points. Classic roan is dominant — homozygous roan may be embryonic lethal.

Silver (PMEL17)

Specifically dilutes eumelanin (black pigment) to a silver or chocolate colour. Affects black points in bay horses and the entire coat in black horses. Can produce silver dapple when combined with grey.

Champagne (SLC36A1)

A dominant dilution gene that dilutes both eumelanin and pheomelanin, producing gold (chestnut base), amber (bay base), or classic champagne (black base). Often confused with Cream.

Tobiano / Overo spotting (KIT, EDNRB)

White spotting patterns. Tobiano produces large white patches crossing the topline. Overo patterns (including frame overo) produce irregular white patches on the belly and sides. Frame overo homozygotes are often lethal.

For advanced equine genetic testing covering all these loci, the UC Davis Veterinary Genetics Laboratory offers comprehensive horse colour panels.

Frequently Asked Questions — Horse Coat Colour Genetics

What genes control horse coat colour?

Three primary gene loci control most horse coat colours. The Extension locus (MC1R gene) determines whether black pigment (eumelanin) can be produced at all. The Agouti locus (ASIP gene) controls whether black pigment is distributed throughout the coat (black) or restricted to points like mane, tail, and legs (bay). The Cream gene (SLC45A2/MATP) acts as a dilution modifier, lightening the base coat colour. One Cream copy produces palomino or buckskin; two copies produce cremello or perlino.

How does the Extension locus determine base coat colour?

The Extension locus (MC1R gene) is the primary switch for black versus red/chestnut pigmentation. Horses with at least one dominant E allele (EE or Ee) can produce eumelanin (black/brown pigment). Horses with two recessive e alleles (ee genotype) cannot produce eumelanin and can only make pheomelanin, resulting in chestnut colouring — a reddish-copper coat with no black pigment anywhere. The e allele is sometimes called the "chestnut allele".

What is the difference between bay and black horses genetically?

Both bay and black horses have at least one dominant E allele at the Extension locus (they can produce black pigment). The difference is at the Agouti locus (ASIP gene). Black horses are homozygous recessive at Agouti (aa genotype), allowing black eumelanin to be deposited throughout the entire body. Bay horses carry at least one dominant A allele (AA or Aa), which restricts black pigment to the points — mane, tail, lower legs, and ear tips — while the body becomes brown or reddish-brown.

Can two chestnut parents produce a bay or black foal?

No. Two chestnut parents are both ee genotype at the Extension locus. They can only pass on the e allele. All their offspring will also be ee — and therefore chestnut. Chestnut is recessive for the Extension locus. This is one of the most reliable rules in horse colour genetics: chestnut × chestnut = always chestnut.

How does the Cream gene produce palomino and buckskin?

The Cream gene (SLC45A2 gene, also called MATP) is an incomplete dominant gene. One copy (heterozygous, nCr) dilutes the base colour: chestnut becomes palomino (golden body with white or cream mane and tail), bay becomes buckskin (golden body with black points), and black becomes smoky black (appears similar to black but may have a slightly faded appearance). Two copies (homozygous, CrCr) produce a much stronger dilution: chestnut becomes cremello (cream coat with blue eyes), bay becomes perlino, and black becomes smoky cream.

Can two palomino horses produce a cremello foal?

Yes. Palomino horses are genotype ee (chestnut base) + nCr (one Cream gene). When two palominos are crossed, the Cream gene follows a simple 1:2:1 ratio: 25% chance of nN (chestnut), 50% chance of nCr (palomino), and 25% chance of CrCr (cremello). So two palomino parents have a 25% probability of producing a cremello foal, a 50% chance of palomino, and 25% chance of chestnut.

What other horse colour genes are not included in this calculator?

This calculator models the three primary base colour genes (Extension, Agouti, Cream). Additional modifying genes not included are: Grey (greying with age, caused by STX17 gene), Dun (primitive striping dilution, ASIP-related), Roan (mixed white and coloured hairs, KIT gene), and spotting patterns — Tobiano, Overo, Frame Overo, Sabino, and Splashed White (all involve KIT or EDNRB genes). Pearl, Champagne, and Silver (PMEL17) are additional dilution genes also not modelled here.