The base coat colours of the horse are chestnut, bay and black. All other colours and patterns are created by genes that modify or add some form of white pattern to the base colours.
Coat colour is determined by the relative amounts of the pigment’s eumelanin and pheomelanin, which are both types of melanin. Eumelanin is a dark pigment responsible for the black coat colour and brown based hues, while pheomelanin is red and in horses causes the chestnut coat colour.
The amount and distribution of these two pigments on the coat is determined by two genes: ASIP and MC1R.
Firstly, we will consider chestnut coat colour, which is determined by the gene called MC1R, of the melanocortin 1 receptor. The symbol for the alleles of this gene are ‘E’ and ‘e’. E stands for extension, one of the alternate names for this genetic test, which is also sometimes called red factor or red/black.
Chestnut horses have a single base change in both copies of their MC1R gene that triggers the pigment cells to only produce phaeomelanin. Horses carrying two copies of this recessive ‘e’ variant will only have red pigment and will be chestnut. This action is independent of the ASIP gene. This horse would have the genotype ‘ee’ at this locus.
A research paper in 2000 reported on a second chestnut allele. It is called ‘ea’ and acts in the same way as the normal e allele does. It is located only a couple of basepairs downstream of the e allele, so it is linked to it. It is also very rare, only being identified in a few breeds including German Black Forest horses. Because it is linked to the normal e allele, we don’t offer a test for this specific variant.
If the horse is not chestnut, it must have one or two ‘E’ alleles, allowing the cells to produce eumelanin. This permits the presence of black or dark pigment in its coat. The distribution of black is dependent on another gene called agouti-signaling protein (ASIP), which is often just called agouti. The two variants of agouti are ‘A’ and ‘a’.
If a horse has one or two ‘A’ alleles, the black colouring is restricted to the points of the horse, and it is bay. The genotype of a bay horse is E-/A-. The dashes indicate unknown alleles. If the horse is not chestnut, and only has the recessive ‘a’ ASIP allele, it will be black. Its genotype will be E-/aa.
While we have a good understanding of how these base colours are inherited, there is still a lot that is unknown. Genetically speaking, there are no brown horses, they are either dark bay or faded black. So why do some horses look brown? Recent research has indicated that there are other genes that can alter the base colours to create dark bay and liver chestnut. This will be discussed in another article.
Why would you order these tests?
You may not be able tell your horses base coat colour if your horse is grey, double dilute, or has a white spotting pattern covering much of its coat. In that case, you would order both tests. Alternately, you might be interested to know if your chestnut horse can have a black foal (with the agouti test), if your black horse can have a chestnut foal (with the red factor test), or if your bay horse can have non-bay coloured foals (using both tests).
The base coat colours: A bay horse with a red coat and black legs, mane and tail (E-/A-) on the left; a chestnut horse with a completely red coat (ee/--) in the centre, and a black horse (E-/aa) on the right.