Horse Coat Color Loci: What Each Gene Does

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By Bikash Roy

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Bikash Roy

Online Research Specialist · SEO Strategist · Web Developer

Bikash personally verifies every calculator against official standards (WHO, NIH, government data). Online research specialist, SEO strategist, and web developer with 10+ years building accurate digital tools.

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· August 17, 2026

The single most useful idea in equine color genetics: a gene can be present and do nothing visible. Almost every “surprise” foal comes from that, and the horse color calculator models it by letting you set genotypes rather than pick a color.

Base color comes first

Extension (E locus) decides whether black pigment can be made at all.

• e/e — no black pigment anywhere. The horse is chestnut, whatever else it carries.
• E/E or E/e — black pigment is possible, and Agouti then decides where it goes.

Agouti (A locus) only matters on a horse that can make black pigment.

• A/_ — black restricted to the points: mane, tail, legs, ear edges. Bay.
• a/a — black across the whole body. Black.

On a chestnut, Agouti is completely invisible and still inherited normally. That is why the calculator disables the Agouti selector once you choose e/e — not because the gene is absent, but because it has nothing to act on.

Dilution genes

Cream is the one where copy count changes the answer rather than just the strength — one copy and two copies give different named colors, not the same color more intensely.

Silver is the classic invisible passenger. It needs black pigment to act on, so a chestnut can carry it, pass it on, and show nothing. When it lands on a black or bay foal it looks like it appeared from nowhere — the subject of why horse colors seem to skip a generation.

Whitening genes

Grey (G) causes progressive whitening with age over any base color. A grey horse is born its base color and lightens over years. Grey is not a base color; it is a process layered on top of one.

Roan intermixes white hairs through the body coat while leaving the head and legs largely unaffected. Unlike grey it does not progress — a roan stays roan.

Spotting patterns

Tobiano, frame overo, and the Appaloosa/leopard complex each produce white patterning through different mechanisms.

Frame overo carries the one genuinely dangerous interaction in this whole system. It is dominant, so a single copy (O/n) produces a healthy, normally patterned horse. Two copies (O/O) produce a foal with Overo Lethal White Syndrome, which is invariably fatal within days. Two carriers bred together have a one-in-four chance of that outcome on every foal, which is why frame overo and lethal white testing is the page to read before any pairing that could involve it.

Reading a genotype

Notation is consistent once you know it:

• Uppercase is the dominant allele, lowercase the recessive: E over e, A over a
• n means “no copy of this variant” — n/Z is one silver allele, n/n is none
• Two identical letters is homozygous; two different is heterozygous and hides something

The heterozygous results are the ones that matter for breeding. E/e looks identical to E/E on the horse and behaves completely differently in a foal. Working through a real panel line by line is covered in reading a horse coat color DNA panel result.

What a predictor cannot do

This calculator shows how the genes interact once you know the genotypes. It cannot tell you what your horse actually carries — not the hidden e in a bay, not a single copy of frame overo in a horse with minimal white.

For any breeding decision, and particularly any pairing where frame overo is possible, use an accredited DNA panel. UC Davis VGL is the standard reference lab and publishes exactly which variants each panel covers.