The basic colour families of the horse are the colours which are defined by the two genes that control the expression of red and black/brown pigment, these are:

• Black: the colour is defined by the expression of the black pigment eumelanin. 
• Chestnut: the colour is defined by the expression of the red pigment pheomelanin. 
• Bay: the colour is defined by the expression of both red and black pigments.

Some horses are impossible to classify in these families, as the basic colour is unrecognisable due to a certain modification in colour expression, examples include grey, white or highly diluted colours. However, these modifications are rarely very dramatic and still lead to recognisable variations of the basic colours.

Variation of the basic colours

• Colour modification may be in the form of nuances or shades. These variations are generally slight, for example producing light and dark bays. These modifications are either not on a genetic basis, or the genetic basis is not (yet) fully identified.
• Other forms of colour variation are known to be the result of colour modification through genetic factors, for example producing a dun from a bay or a palomino from a chestnut.

Genetics behind the basic colours: the E gene

This is known as the extension gene. This gene controls the "extension" of black pigment across the body. The dominant form is E, in which black pigment extends across the entire body (resulting in a black horse), the recessive form is e, in which no black pigment is expressed on the body leaving only the red pigment visible (resulting in a chestnut horse). 

As there are always a pair of genes for every trait, a horse may be either EE (black), Ee (black) or ee (chestnut).

Genetics behind the basic colours: the A gene

This gene is known as the agouti gene. This is a modifying gene, and as all horses have it, it is known as the common modifier. The dominant form of the gene is A, which restricts the black pigment (imparted by the E gene) to the mane, tail and distal limbs of the horse. The coat is left with the red pigment. This results in the colour bay. The recessive form a does not have any effect on the black pigment.

Genetics behind the basic colours: the A gene

This results in the following possible basic colour gene combinations:

• AA and Aa combined with the genes EE or Ee results in a bay horse (the black pigment is present and modified). 
• AA and Aa combined with the genes ee results in a chestnut horse (there is no black pigment to modify). 
• aa combined with the genes EE or Ee results in a black horse (the black pigment is present and not modified).
• aa combined with ee results in a chestnut horse (there is no black pigment and no modification).