Coat Colour Genetics – A Basic Guide


This week’s blog on the genetics of horse coat patterns is courtesy of Lindsay Barker, B.Sc.

No good horse is a bad colour is a very common saying but lots of people have their own preferences and that’s ok too.  But do you know what colour your horse actually is? We as horsepeople like to have our own terms for colours, like piebald and skewbald but it doesn’t reflect what the horse genetically is (and how it might be passed on).

So every horse on the face of the planet is either black or chestnut.

Yup, it’s true.  Your palomino pintaloosa out in that field is hiding his true identity.  Every coat pattern and colour is caused by different dilutions or modifiers that change how this black or chestnut horse looks.

So we have to go back to high school a little here and talk about some basic Mendelian genetics.  You have some genes that are dominant and recessive to each other, these are often written as a capital letter and a lower case letter so keep it straight forward.

AA – homozygous for the dominant trait

Aa – heterozygous for the trait but phenotypically it would show the dominant trait (aka it would look like it was homozygous for the dominant trait because the dominant masks or hides the recessive gene)

aa – homozygous for the recessive trait

You can also have genes that are incomplete dominant, where the heterozygous trait has a different phenotype than the other two homozygous forms.  All three combinations will look different.

AA – homozygous for the dominant trait

Aa – heterozygous for the trait and phenotypically (look) different from the homozygous forms

aa – homozygous for the recessive trait

So in horses the gene controlling the base colour is called the Extension gene, the base pigments are black (E – dominant) and red (e – recessive).  A black horse can be either be EE or Ee and the chestnut horse will only be ee.




This Canadian is black (genetically he’s going to be be EE or Ee).







This Thoroughbred is chestnut (genetically she’s ee).







One of the most common horse colours is bay, so how do we get there from black or chestnut horse.  Bay and Brown are caused by the Agouti gene which is dominant, and it controls how the black pigment is distributed over the horse’s body.  AA or Aa causes the black pigment to move only to the horses’ points (legs, ears, mane and tail) and the aa causes the pigment to be uniformly distributed on the horses body.  The Agouti gene has no effect on the red pigments.

So your black horse (EE or Ee) will be bay or brown if it is AA or Aa, and stay true black only if it is aa. The chestnut horse (ee) can be everything (AA, Aa or aa) and still remain chestnut.



This Thoroughbred is bay (genetically he’s going to be EEAA, EeAA, EeAa or EEAa).








So we’ve laid out our 3 basic coat coats – black, bay/brown and chestnut.  This is where we have another series of genes that dilute our basic colours to give us colours like palomino or red dun.  These genes are Cream (incomplete dominant), Dun (dominant), Champagne (dominant), Silver (dominant – no effect on red pigment), and Pearl (recessive).


The Cream gene is probably the most well known of the different dilution genes. This incomplete domination gene, which means the homozygous form and the heterozygous form of Cream will look visually different.  In the Cream gene the heterozygous form (Cr/n) is known as a single dilute where the homozygous form (Cr/Cr) is often referred to as a double dilute.  Cream is interesting because although it has the ability to lighten both the red and black pigments, it really only affects black in the double dilute form.

Black horse (AAee or Aaee) with Cr/n – Smokey black

Black horse (AAee or Aaee) with Cr/Cr – Smokey cream

Bay horse (AAEE, AAEe, AaEE, AaEe) with Cr/n – Buckskin

Bay horse (AAEE, AAEe, AaEE, AaEe) with Cr/Cr – Perlino

Chestnut horse (aaEE, aaEe, aaee) with Cr/n – Palomino

Chestnut horse (aaEE, aaEe, aaee) with Cr/Cr – Cremello



This cute fellow is a Palomino (genetically he’d be aaEE-Cr/n, aaEe-Cr/n, aaee-Cr/n)








Dun is very distinguishable by its dorsal stripe, darker legs, primitive markings (like a shoulder stripe or stripes on the legs), darker head, mane and tail. The Dun gene is a dominant one and it affects both the red and black pigments on a horse’s coat. It lightens up the horse’s base body colour often while keeping the undiluted colour visible on the legs, head, mane, tail and the dorsal stripe.  So a horse with D/D or D/d will be dun and one with dd cannot be dun.

Black horse (AAee or Aaee) with D/D or D/d will be a blue dun, black dun or grullo (all the same colour just we have lots of fancy names in different breeds).

Bay horse (AAEE, AAEe, AaEE, AaEe) with D/D or D/d will be a classic dun, bay dun or zebra dun (again all the same actual colour just different names).

Chestnut horse (aaEE, aaEe, aaee) with D/D or D/d will be a red dun.



This is what a grullo/black dun would look like – this is actually just a clipped black horse – which is why it is important to get a genetic testing done on a horse if you intend to breed and colour is important to your program.







Champagne is newer discovered gene, because of its similarity to the effects of the cream, pearl and dun dilutions but there are some pretty big differences if you know what you are looking for. Often horses will be born with blue eyes and then they change to an amber or hazel as the horse ages.  They also have pink mottled or freckles skin that darkens with age and a shiny coat that often darkens in the winter.  Champagne works by diluting the entire coat colour of the horse uniformly on both red and black pigments, so what colour the horse turns into is based on what its base colour is.  It is a dominant gene so a horse with Ch/Ch and Ch/n will show the champagne effects on coat colour, where a horse with nn will not be champagne.

Black horse (AAee or Aaee) with Ch/Ch or Ch/n – classic champagne, a uniformly lightened black coat.

Bay horse (AAEE, AAEe, AaEE, AaEe) with Ch/Ch or Ch/n – amber champagne, uniformly dilutes the bay colour, so the body is a lighter brown and the points are a lighter black/dark brown.  Sometimes referred to as an amber buckskin.

Chestnut horse (aaEE, aaEe, aaee) with Ch/Ch or Ch/n – gold champagne, uniform dilute of chestnut to a gold colour, and often the mane and tail are lighten slightly more giving it a very similar appearance to palomino.

genetics genetics


This horse may be a palomino or may be gold champagne – this is where genetic testing would solve the mystery. Her eyes are more amber which leads towards champagne but she doesn’t have mottled skin so maybe she’s palomino.






Silver is an interesting gene because it only affects the black pigments (like how the Agouti gene has no effects on chestnuts).  It causes black areas of the horse to go much lighter which is where the term silver comes from.  It is a dominant gene so horses would show the colouration with either Z/Z or Z/n if they had black in their base coat, and a horse with Z/Z or Z/n with a red based colour would not show any silver (the gene is hidden).

Black horse (AAee or Aaee) with Z/Z or Z/n will be a chocolate colour with flaxen mane and tail, often misleadingly called a chocolate palomino.

Bay horse (AAEE, AAEe, AaEE, AaEe) with Z/Z or Z/n will be a bay with lighter points and a flaxen mane and tail (silver bay).

Chestnut horse (aaEE, aaEe, aaee) with Z/Z or Z/n will just be chestnut.


The Pearl gene is the newest discovered gene that can be tested.  It seems to be the rarest of the dilutions, however it has been regularly referred to in Quarterhorses as the Barlink Factor. This one is a little different because it’s recessive so it only shows up if the individual has two copies of the pearl gene.  Similar to how chestnut can “hide” under a black or bay based coat.  When a horse carries two copies of the Pearl gene, their coat, mane and tail will be lightened as well as having lighter eye colour.  It is very similar to how Champagne effects coat colour but it does not affect the skin pigment (no pink mottled skin that darkens over time). Now this is where this gene gets a little complicated, although it is recessive so will only show if both copies of Prl are present, it interacts with the Cream gene if it is also present.  If one copy of Cream is present and one copy of Pearl is present, the horse will look almost identical to a Cream double dilute.

Black horse (AAee or Aaee) with Prl/Prl – lightened black

Bay horse (AAEE, AAEe, AaEE, AaEe) with Prl/Prl – lightened bay colour with lightened black/dark brown points

Chestnut horse (aaEE, aaEe, aaee) with Prl/Prl – lightened chestnut

Cream interactions with Pearl

Black horse (AAee or Aaee) with Prl/n AND Cr/n – similar to smokey cream

Bay horse (AAEE, AAEe, AaEE, AaEe) with Prl/n AND Cr/n – similar to perlino

Chestnut horse (aaEE, aaEe, aaee) with Prl/n AND Cr/n – similar to cremello

So about that palomino pintaloosa sitting in the field, you know it’s ee (chestnut base) with one copy of the Cream gene (Cr/n) that makes it palomino.  Well what about the pintaloosa?  Stay tuned for next time when we discuss patterns and depigmentation like pinto patterns, appaloosa patterns and greys.

June 6, 2016 |

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