B A S E S
To clarify once and for all, horses have three base colors - bay, black, and red. These colors are controlled by two gene loci, MC1R on Chromosome 3 and ASIP on Chromosome 22. MC1R, also called extension, controls the type of pigment allowed into the hair shaft. The dominant allele, E, allows red and black pigment and the recessive allele, e, allows only red pigment. ASIP, also known as agouti, controls the distribution of black pigment in the hair. The dominant allele, A, restricts black pigment distribution while the recessive allele, a, allows black pigment to cover the entire body.
Many people mistakenly think of bay as a modification of black, but this is not true from a genetic standpoint. The extension and agouti genes are co-dependent. Dominant extension needs a recessive agouti allele in order to produce a black coat. Dominant agouti needs a dominant extension allele to in order to produce a bay coat. Research has also shown that the original color of all ancient horses was actually bay dun (EE AA DD).
Many people mistakenly think of bay as a modification of black, but this is not true from a genetic standpoint. The extension and agouti genes are co-dependent. Dominant extension needs a recessive agouti allele in order to produce a black coat. Dominant agouti needs a dominant extension allele to in order to produce a bay coat. Research has also shown that the original color of all ancient horses was actually bay dun (EE AA DD).
B L A C K
Black horses require at least one dominant extension allele and also to be homozygous recessive for agouti (not "no agouti," as agouti is a locus and all horses have it, they possess either dominant or recessive alleles). Black, like all other coat colors, can vary in shade. Some blacks can fade in the sun and be confused for bays, but a good rule of thumb is to look at the hair around the muzzle. Black horses generally will not fade much around the face and won't have brown or tan hairs around the nose.
EE aa or Ee aa
R E D
Red color in horses requires being homozygous recessive for extension. A red horse can have dominant or recessive alleles on agouti, but research has shown that it does not have any effect on a red coat at all. There are many shades of red that have not been linked to any genetic factor. Some red horses can be so dark they can appear black, but the coronet area on red horses will always be some degree lighter than the rest of the hair. Red horses may be called chestnut, sorrel, liver, and more, but they are all the same genetically.
ee AA or ee Aa or ee aa
B A Y
The bay color requires a dominant extension and dominant agouti allele. The "traditional" bay coat is a reddish-brown color with black legs, mane, and tail. Bay can come in many different shade variations as well, the terms for which are subjective. A very dark shade with tan around the muzzle, eyes, flanks, and other soft body parts is often called brown or seal bay/brown. There is another shade variation where the black on the legs only reachest the fetlocks, which is called wild bay. However, there is no genetic distinction between these shades.
In recent years there was a test available for a fake allele on agouti that was called At. The test was based on mouse genetics and produced many false results, ending in the entire lab being shut down after the creator of the test admitted to its inaccuracy. Geneticists have completely mapped the agouti locus and there exists only dominant A and recessive a. There is no additional allele for either the brown or wild bay phenotypes. If there is any genetic factor for them, they are not a part of agouti.
In recent years there was a test available for a fake allele on agouti that was called At. The test was based on mouse genetics and produced many false results, ending in the entire lab being shut down after the creator of the test admitted to its inaccuracy. Geneticists have completely mapped the agouti locus and there exists only dominant A and recessive a. There is no additional allele for either the brown or wild bay phenotypes. If there is any genetic factor for them, they are not a part of agouti.
EE AA or EE Aa or Ee AA or Ee Aa