Horse coat colour genetics

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Horses coat colours are determined by information stored in their DNA. DNA is usually a tangled mass of strands that occupies the nucleus of cells. When cells are about to divide, however, the DNA is tidied up into bundles known as chromosomes. Horses DNA arranges itself as 64 chromosomes (humans = 46). These chromosomes are paired, with each chromosome of the pair carrying the same pattern of genes.
Genes are sections of DNA that affect characteristics of the animal. The pairing of chromosomes means that there are two copies of each gene in animal cells. These two copies may be the same, or they may differ. The different forms that a gene can take are called alleles.
Alleles are usually either dominant or recessive. The dominant allele will be expressed (i.e. will determine the characteristic) when it is paired with another identical dominant allele, and also when it is paired with a different, recessive, allele. Dominant alleles are usually symbolised using a capital letter. Recessive alleles will only be expressed if they are present as two identical copies. Recessive alleles are given small letters.
Egg cells and sperm cells contain half of the chromosomes of the other body cells, one chromosome from each pair. Animals inherit half their chromosomes (and therefore half their genes) from their mother, and the other half from their father. When the maternal and paternal chromosomes come together as one cell, that cell (the embryo) will carry one allele from its mother and one allele from its father for each gene. This results in combinations of alleles occurring in the offspring that may not occur in either the mother or the father individually.


In horses, there are a number of genes that influence coat colour. Each of these genes has two or more different alleles (forms). All horses carry all the coat colour genes, however there is a hierarchy of expression, with some genes masking the effects of others in some animals. The different genes act together to produce the final, visible, coat colour of the horse.

The first gene in the hierarchy of coat colour is the albino gene, ‘W’.
If a horse has just one copy of the dominant W, it will mask to all other coat colours and the horse will be albino (pink eyes and skin, white hair). The horse will carry genes for a variety of other coat colours, but these do not show through in its actual physical colour.
Albinism occurs in many animal species, including humans, and it causes problems in most. Albinos are very sensitive to sunlight and may have poorer vision than their peers. This alone makes albino animals relatively rare – they are not purposely bred very often, however albino horses are extremely rare because of a twist in the equine albino genes tale – horses that inherit two copies of W die just before or just after birth – ‘WW’ is lethal. For a WW horse to be produced, both its parents would have to be albino, so thankfully this situation is usually avoidable.
If a horse is ‘ww’, it will not be albino. Most horses are ww.

The next gene in the hierarchy is the grey gene, ‘G’. Grey, G, is dominant to non-grey, g. Horses that carry the G allele will be grey. Horses that are gg (no pun intended) will be any colour except grey. Horses that carry two copies of G will always breed grey foals. If a horse carries only one copy of G (i.e. it is Gg), each foal will have a 50% chance of being grey (rising to 75% if its other parent is also Gg). A tool called a Punnett Square is a useful way to visualise this:

(N.B Apologies for all the stupid dots, the site keeps trying to rearrange things and get rid of all the spaces, obviously thinks the letters are lonely which is a bit frustrating......)

Parents GG (grey) and gg (non-grey

.................G......... G

g .............Gg ........Gg
..............grey ........grey

g............. Gg......... Gg
...............grey ........grey

All foals have grey coat colour.


Parents Gg (grey) and gg (non-grey)

..............G.......... g

g ..........Gg .........Gg
...........grey ..........grey

g.......... Gg.......... gg
............grey .....non-grey

There is a 50% chance that each foal will be grey, and a 50% chance it will be non-grey.

Parents Gg (grey) and Gg (grey)

.................G ..............g

G............ Gg............ Gg
...............grey .........grey

g ..............Gg ...........gg
................grey ......non-grey

There is a 75% chance that each foal will be grey, and a 25% chance it will be non-grey.

All genetically grey horses begin life with a coloured base coat that turns grey when their foal coat is shed. The coat colour comes in a very dark steel grey which always fades as the horse ages.

The next layer is a little more complex than the first two. This is the bay/black/chestnut layer – the last of the possible base coat colours. These three coat colours result from the combined action of two different genes, extension, ‘E’ and agouti, ‘A’.
The extension gene controls the pigment colour in hairs. The dominant E gives black pigment in the hair; the recessive e gives red pigment.
The agouti gene controls the positioning of black hair around the body. The dominant A restricts black to the points (nose, ears, legs, mane and tail), the recessive allele a gives an even coverage of black all over the horse.

Chestnut horses are all ‘ee’, and the A gene has no effect on their colour. Agouti will ONLY affect black hair, and chestnuts have no black hair to be restricted. Chestnut is the only guaranteed true-breeding colour – if you cross two chestnut horses, you will get a chestnut foal (unless any gene mutation occurs, but that’s another story!).
Black horses must have at least one copy of the ‘E’ allele along with ‘aa’ which means that the black is evenly distributed all over the body.
Bay horses must have at least one copy of the ‘E’ allele along with at least one copy of the ‘A’ allele which restricts the black hair to the points.

Try the Punnett Square for yourself and see what the possible outcomes of mating two bay horses might be!
The first box in the Punnett Square is filled in for you.
Remember
- all chestnuts are ee, with any combination of agouti alleles
- all black horses must have at least one E, but are aa
- all horses that have at least one E along with at least one A are bay.

Can you see why bay horses occur so regularly?

Mating two bay horses that are ‘AaEe’

Parents ....... .........AaEe x AaEe

Sperm/Egg ...AE/ Ae/aE/ ae and AE/Ae/aE/ae

Offspring

............................AE ...................Ae................... aE .....................ae

AE ....................AAEE............... AAEe............................................
............................bay........................................................................
Ae ....................................................................................................
...........................................................................................................
aE ....................................................................................................
.........................................................................................................
ae......................................................................................................
..........................................................................................................

These are the five basic coat colours - albino, grey, bay, black or chestnut.
All other colours are the result of the actions of other genes on these basic colours. These genes are divided into ‘dilution’ genes and ‘pattern’ genes.

Dilution genes

The cream gene, ‘C’ has an effect on bay and chestnut horses.
It shows INCOMPLETE DOMINANCE i.e. unlike the genes we have looked at so far, horses that are Cc are different to those that are CC.
Horses that carry the cc alleles show no dilution – they remain bay or chestnut.
Chestnut horses with one copy of the C allele are diluted to palomino. Chestnut horses with two copies of the C allele are diluted to cremello (pale horse with blue eyes).
Bay horses with one copy of the C allele are diluted to buckskin (although in the UK this is usually (wrongly) called yellow dun – we will get to duns shortly).
Bay horses with two copies of the C allele are diluted to perlino (also pale with blue eyes – difficult to tell the difference between this and a cremello without knowing parentage).
The effect of incomplete dominance is that neither palominos nor buckskin horses breed true. Crossing two palominos (we will stick to palomino for simplicity – buckskins follow exactly the same pattern of inheritance) will give only a 50% chance of producing a palomino foal, with a 25% chance of a chestnut being born and a 25% chance of producing a cremello. The only way to guarantee production of a palomino foal is to cross a chestnut and a cremello.
Punnett Squares should help to visualise this:

Palomino x Palomino

...................C ..............c

C ...............CC ............Cc
..............cremello.... palomino

c ................Cc............. cc
..............palomino... chestnut

There is a 50% chance that each foal bred will be palomino, a 25% chance it will be chestnut and a further 25% chance that it will be chestnut.

Chestnut x Palomino

........................c.................... c

C ...................Cc.................. Cc
.................palomino .........palomino

c ....................cc ...................cc
................chestnut............. chestnut

There is a 50% chance that each foal bred will be palomino, and an equal chance that it will be chestnut.

Cremello x Chestnut

..........................C......................C

c....................... Cc ...................Cc
....................palomino .........palomino

c .......................Cc..................... Cc
...................palomino.......... palomino

All foals will be palomino, bearing in mind that neither of the parents were this colour.

The dun, ‘D’, gene has an effect on all colours. The D gene dilutes body hair but not hair at the points, giving the dun effect e.g. mouse dun is diluted black, yellow dun is diluted bay, red dun is diluted chestnut. Horses diluted are a result of dun, rather than cream, have darker mane, tail, nose, ears and legs (which may have zebra stripings), and also have a dark ‘eelstripe’ along their backbone. Buckskins and yellow duns appear similar, however the eelstripe should distinguish between them. D is a dominant gene.

Pattern genes
The ‘TO’ gene produces tobiano patterning. In the UK this would be referred to as piebald or skewbald, but these terms don’t reflect the genetics of the colour so we will stick to Americanisms. A horse is tobiano if it has white across its backbone. Tobiano is a dominant gene. As with other dominant genes, the TO gene will be expressed in horses that carry TOTO and also in those that are TOto. If a horse carries two identical alleles for one gene (e.g. TOTO), it is termed ‘homozygous’ for that gene. If the alleles are different (e.g. TOto), the horse is termed ‘heterozygous’ for that gene. A test for homozygosity has now become available, due to the increased value that can be commanded by a homozygous TO animal. Previously, and still for many, the only way to distinguish between homozygous and heterozygous was by looking at the offspring of the horse in question. If a coloured stallion has produced a large number of coloured offspring there will be a high probability that he is TOTO, and therefore will always breed coloured horses. If, however, a coloured stallion has produced even one solid coloured foal, he must be heterozygous (TOto) and therefore is not guaranteed to produce a coloured foal even when bred to a coloured mare. This is why breeders advertise their coloured stallions as ‘homozygous’ – they are guaranteeing a coloured foal from a mating with their stallion. Again, Punnett Squares can help to clarify this:

Homozygous tobiano x solid horse

...............................TO ...................TO

to ..........................TOto ................TOto
..............................tobiano............ tobiano

to ..........................TOto................. TOto
...............................tobiano........... tobiano

All foals will be tobiano.

Heterozygous tobiano x solid horse

..............................TO............................. to

to ..........................TOto.......................... toto
..............................tobiano ......................solid

to ..........................TOto........................... toto
.............................tobiano......................... solid

Each pregnancy has a 50% chance of producing a tobiano (coloured) foal and a 50% chance of producing a solid foal. None of the coloured foals produced will breed true for the coat pattern – they will all be heterozygous for TO.

Homozygous tobiano x Heterozygous Tobiano

...............................TO .......................TO

TO ........................TOTO................. TOTO
..............................tobiano ...............tobiano

to ...........................TOto ...................TOto
..............................tobiano................. tobiano

All foals will be tobiano, however only there is only a 50% chance that these foals will breed true for the coat colour.

Heterozygous tobiano x Heterozygous tobiano

...................................TO .......................to

TO ..........................TOTO ..................TOto
.................................tobiano................ tobiano

to ..............................TOto..................... toto
................................tobiano ...................solid

At each breeding, there is a 75% chance that the foal produced will be coloured and a 25% chance that it will be solid, even though this cross is of two coloured horses.


Whether a horse is piebald (white on black) or skewbald (white on brown/ chestnut) will be determined by the base coat colour genes. It is possible to have a tobiano horse that appears grey – in this case the ‘tobiano areas’ will be pink skin, with the rest of the skin being grey. This may only become obvious when the horse is soaking wet!

The ‘O’ gene produces overo patterning. A horse is overo if its white areas do not cross its backbone – it looks as if it has been dipped in paint rather than splashed with it. Overo is also a dominant gene, however it follows the same pattern as albino in that foetuses that inherit two copies of O will die in utero and be reabsorbed by the mother.
The most common breed in the UK to show overo colouring is the Clydesdale.

Tobiano and overo patterning are more common in America than in the UK. Combinations of the two genes may occur, the result being an almost fully white horse with small areas of base colour. These can be as extreme as the ‘medicine hat paint’ – a horse that is white with only the ears and a small patch around the poll area showing the base colour!

The ‘LP’ gene produces leopard pattern, or the appaloosa pattern. It is a dominant gene that shows many different variations.
The ‘RN’ gene produces a mix of white and coloured hair i.e. roan. It is also dominant and also lethal if present in two copies (although there is recent evidence for viable homozygous roan animals, in quarter horses at least). Basic black coat colour with the roan gene produces blue roan, chestnut produces strawberry roan.

Bizarre and wonderful combinations of these base colours and pattern genes are possible – blue roan appaloosa tobiano, red dun overo, palomino medicine hat.

White markings on the face and legs are controlled by a separate set of genes that show a different kind of inheritance to those discussed so far. They can be though of as ‘additive’. If you breed from two horses with very small or no white on their bodies, you will get a foal with virtually no white. Conversely, if you breed from two horses with white faces and a lot of white on their legs, your foal will inherit similar. If once parent is minimally marked and the other has a lot of white, the foal will be somewhere in between. This is termed polygenic inheritance – genes that govern things like height and weight also follow this type of pattern. Most characteristics of animals are controlled by polygenic traits, and are also influenced heavily by the environment. Coat colour is one of the few visible traits on which the environment has little effect – although it’s rare to be certain of the outcome of any breeding project, at least coat colour can be predicted with a reasonable amount of certainty!

Bibliography/ Further Reading

Bowling, A (1996) Horse Genetics, CAB International, Oxon
http://www.equinecolor.com/unusual.html

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