Knowledge · Coat colours in horses

Understanding coat colours: how colour is inherited in horses

A horse's coat colour follows clear genetic rules. Two genes set the base colour: chestnut, bay or black. Further genes dilute it, mix in white hairs or create spotting patterns. Many of these variants stay hidden and only show up in the offspring. Some are also linked to health risks. This article explains how the colour genes work together, when a DNA test makes sense and which variants Generatio tests for.

View testable variants Health relevance

Why test for coat colour?

What you see on a horse is only part of what it passes on. A black horse can carry chestnut, and a chestnut can carry a dilution that stays invisible on its own coat. A DNA test makes these variants visible, regardless of age, season and coat condition.

Documentation

Identify the colour reliably

Foal coats are misleading, greys lighten over the years, and some shades look almost identical. The genotype gives you an unambiguous colour description for the studbook, the equine passport and sales documents.

Hidden variants

See what cannot be seen

Recessive variants such as chestnut, Pearl or Mushroom only show with two copies. Others are masked: Silver is invisible on a chestnut, and Cream is barely visible on a black horse. Minimally marked pintos are often not recognised as such either.

Breeding plans

Predict foal colours

Once the genotypes of both parents are known, the possible foal colours and their probabilities can be calculated. A homozygous horse passes its variant on to every foal. That is essential for targeted colour breeding.

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Main genes and modifiers

Every horse colour is built on two pigments: black eumelanin and red pheomelanin. Two main genes determine which pigment is produced where. This gives the base colour. All other colour genes change this base colour and are therefore called modifiers. The underlined names lead to the corresponding article in the lexicon.

The base colour: two genes, three colours

Main gene · MC1R

Extension (E locus)

Extension decides whether a horse can produce black pigment in its coat at all. The dominant allele E allows black. With two copies of the recessive allele e, only red pigment is produced: the horse is chestnut, whatever is present at the Agouti locus.

Main gene · ASIP

Agouti (A locus)

Agouti controls where the black pigment is distributed. The dominant allele A restricts black to the mane, tail and legs: the horse is bay. With a/a, black stays all over the body: the horse is black. On a chestnut, Agouti is not visible but is still passed on.

How the two genes produce the base colour
Extension	Agouti	Base colour
e/e	any	Chestnut
E/E or E/e	A/A or A/a	Bay
E/E or E/e	a/a	Black

Modifiers: dilution

Dilution genes lighten the pigment. The resulting colour depends on the base colour and on whether one or two copies of the variant are present.

Dilution genes in horses
Variant	Gene	Inheritance	Effect
Cream	SLC45A2	incompletely dominant	One copy gives palomino (chestnut) or buckskin (bay). Two copies give very light horses with blue eyes: cremello, perlino, smoky cream.
Pearl	SLC45A2	recessive	Only visible with two copies or together with one copy of Cream. Located in the same gene as Cream.
Champagne	SLC36A1	dominant	Lightens red and black pigment. Freckled skin and light eyes are typical.
Dun	TBX3	dominant	Lightens the body while the head and legs stay darker. It adds a dorsal stripe and often zebra stripes on the legs. Dun is regarded as the original colouring of the horse.
Silver	PMEL	dominant	Lightens black pigment only, mainly in the mane and tail. Silver stays invisible on a chestnut.
Mushroom	MFSD12	recessive	Lightens red pigment to a dull sandy shade. Known mainly in Shetland ponies.

Modifiers: white hairs in the coat

Grey and roan
Variant	Gene	Inheritance	Effect
Grey	STX17	dominant	The foal is born coloured and greys progressively until the coat appears white. The skin stays dark.
Roan	KIT region	dominant	White hairs are mixed evenly into the body coat while the head and legs stay coloured. The pattern hardly changes with age. Noriker Roan is a separate variant in the KIT gene.

Modifiers: spotting and white markings

Spotting genes prevent pigment cells from reaching certain areas of skin. Skin and coat stay white there. Several spotting genes can reinforce each other.

Spotting genes in horses
Variant	Gene	Inheritance	Effect
Tobiano	KIT	dominant	Large, clearly defined white areas that usually cross the back. The legs are often white.
Frame Overo	EDNRB	dominant, lethal when homozygous	White areas on the flanks and head while the back usually stays coloured. Expression ranges from obvious to barely visible.
Sabino-1	KIT	incompletely dominant	High white legs, a broad blaze and ragged patches on the belly. With two copies the horse is almost completely white.
Splashed White	MITF, PAX3	incompletely dominant	White head, white legs and white belly, as if the horse had been dipped in paint. Often blue eyes. Several variants (SW1, SW2 and others).
Dominant White (W)	KIT	dominant	More than 30 known variants, many limited to individual lines. The amount of white ranges from enhanced markings to a completely white horse. W20 is widespread and enhances other spotting patterns.
Leopard Complex (LP)	TRPM1	incompletely dominant	Leopard spotting as known from the Appaloosa and Knabstrupper. Together with LP, Pattern-1 (PATN1) markedly increases the amount of white.

Linked to a health risk. The symbol takes you to the section “Health relevance”.

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Health relevance

Colour genes control more than pigment. In early development, pigment cells arise from the same tissue as parts of the nervous system, the inner ear and the eye. A colour variant can therefore have consequences there as well. The following genes are known for this.

EDNRB · risk with O/O

Frame Overo: Overo Lethal White Syndrome (OLWS)

Foals with two copies are born white. Their intestine lacks nerve cells and cannot move its contents along. These foals are not viable and die within a few days. Carriers with one copy are healthy, but the pattern is not always recognisable on them. Two carriers produce an affected foal with a probability of 25 %.

Lexicon: Frame Overo

TRPM1 · risk with LP/LP

Leopard Complex: congenital stationary night blindness (CSNB)

Horses with two copies cannot see in dim light or in the dark. The condition is present from birth and does not progress, and daytime vision is normal. Horses with LP also have an increased risk of equine recurrent uveitis (ERU), highest in LP/LP horses.

Lexicon: Leopard Complex

PMEL · risk with Z/n and Z/Z

Silver: Multiple Congenital Ocular Anomalies (MCOA)

Even one copy can cause cysts in the eye, which usually do not impair vision. With two copies, several malformations of the eye occur, including a bulging cornea, changes to the iris and cataracts. Because Silver is invisible on a chestnut, carriers often go unnoticed without a test.

Lexicon: Silver

MITF, PAX3 · depends on variant

Splashed White: deafness

If pigment cells are missing in the inner ear, the horse is deaf. This affects some Splashed White horses, mainly those with a lot of white on the head and blue eyes. For SW2 it is also assumed that embryos with two copies are not viable.

Lexicon: Splashed White

KIT · homozygous, depends on variant

Dominant White: early embryonic loss

For many W variants it is considered likely that embryos with two copies die early in pregnancy. The mare then appears not to be in foal. W20 is an exception: homozygous horses are viable and healthy. Mating two carriers of the same W variant should be avoided.

Lexicon: Dominant White

STX17 · risk with G/n and G/G

Grey: melanomas

Most grey horses develop skin melanomas as they age, often under the tail, around the anus and on the head. They usually grow slowly but can cause discomfort and spread. Homozygous greys turn white faster and have a higher melanoma risk. Loss of skin pigment (vitiligo) also occurs.

Lexicon: Grey

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Colour oracle: which coat colour can the foal have?

Select the two alleles per locus for the dam and the sire: first the base colour (E locus and A locus), then the dilution factors Cream, Pearl, Champagne, Dun, Silver and Mushroom. A dash in a field means that no result is available for this marker. The oracle then leaves it out of the calculation and names it below the result. From the remaining entries it calculates which coat colours are possible in the foal and how likely each one is.

Genotype of the dam

Base colour

E locus allele 1 E locus allele 2

A locus allele 1 A locus allele 2

Dilution factors

Cream allele 1 Cream allele 2

Pearl allele 1 Pearl allele 2

Champagne allele 1 Champagne allele 2

Dun allele 1 Dun allele 2

Silver allele 1 Silver allele 2

Mushroom allele 1 Mushroom allele 2

Coat colour of the dam: Bay

Genotype of the sire

Base colour

E locus allele 1 E locus allele 2

A locus allele 1 A locus allele 2

Dilution factors

Cream allele 1 Cream allele 2

Pearl allele 1 Pearl allele 2

Champagne allele 1 Champagne allele 2

Dun allele 1 Dun allele 2

Silver allele 1 Silver allele 2

Mushroom allele 1 Mushroom allele 2

Coat colour of the sire: Bay

Base colour of the foal

Chestnut 25 %
Bay 56.25 %
Black 18.75 %

Possible coat colours of the foal

Most likely coat colour: Bay (56.25 %).

Bay 56.25 %
Chestnut 25 %
Black 18.75 %

Result not available for both parents and therefore not taken into account: Cream, Pearl, Champagne, Dun, Silver and Mushroom.

Please note

What the oracle calculates and what it does not

The values apply afresh to every single foal and say nothing about the distribution in a small number of offspring. The two base colour genes and six dilution factors are taken into account, provided a result has been entered for both parents. A marker without a result is not treated as clear, it is simply missing from the calculation. Grey and spotting patterns are not included. The oracle shows the visible colour: variants that are carried hidden, such as Silver on a chestnut or a single copy of Pearl, do not appear in the name. The small horse pictures are schematic drawings and only approximate the shade. The figures are only reliable if the genotypes of the parents are known from a test.

Have base colours tested Have dilution factors tested

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Gene variants testable at Generatio

Generatio tests the most important equine colour genes individually or as a package. The packages combine what belongs together and are the easiest way to start. Each entry takes you straight to the test in the shop.

Packages

2 genes

Base colours horse

Extension and Agouti. The package shows whether a horse is genetically chestnut, bay or black and which base colour it carries hidden.

View base colours package

5 variants

Dilution factors horse

Cream, Champagne, Silver, Pearl and Dun. The package shows which dilutions a horse carries, even if they are not visible on the horse itself.

View dilution package

Spotting

Dominant White and spotting patterns horse

The most common variants for Dominant White and spotting patterns. The package clarifies existing white markings and helps prevent unintended carrier matings.

View spotting package

Single tests

All single tests for coat colour in horses
Group	Variant	Gene	Go to test
Base colour	Extension (E locus)	MC1R	Test Extension
Base colour	Agouti (A locus)	ASIP	Test Agouti
Dilution	Cream	SLC45A2	Test Cream
Dilution	Pearl	SLC45A2	Test Pearl
Dilution	Champagne	SLC36A1	Test Champagne
Dilution	Dun	TBX3	Test Dun
Dilution	Silver / MCOA	PMEL	Test Silver
Dilution	Mushroom	MFSD12	Test Mushroom
Roan	Noriker Roan	KIT	Test Noriker Roan
Spotting	Tobiano	KIT	Test Tobiano
Spotting	Frame Overo	EDNRB	Test Frame Overo
Spotting	Sabino-1	KIT	Test Sabino-1
Spotting	Splashed White 1 (SW1)	MITF	Test SW1
Spotting	Splashed White 2 (SW2)	PAX3	Test SW2
Spotting	Leopard spotting (LP)	TRPM1	Test Leopard Complex
Spotting	Pattern-1 (PATN1)	RFWD3	Test Pattern-1
Dominant White	White Spotting W8	KIT	Test W8
Dominant White	White Spotting W16	KIT	Test W16
Dominant White	White Spotting W19	KIT	Test W19
Dominant White	White Spotting W20	KIT	Test W20
Dominant White	White Spotting W21	KIT	Test W21
Dominant White	White Spotting W30	KIT	Test W30

Linked to a health risk. The symbol takes you to the section “Health relevance”.

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