The original ancestral color of the horse was bay dun. All of the other colors found in the equine species are the result of subsequent mutations over thousands of years. Keep in mind that "mutation", when referring to color genetics, does not in this sense mean anything negative, but simply a change from the original genotype.

Horses produce two types of pigment: red and black. All of the other colors are built from these two basic pigment types.

Red and black pigment types are controlled at the Extension locus. There are two possible alleles for each horse at Extension: "E" and "e". Every horse has some combination of the two (either EE, Ee or ee), which determines their basic pigment type. Black (which is written as "EE" or "Ee") is dominant to Red (which is chestnut, written as "ee"); red is recessive to black. This means that if a horse has at least one one dominant Extension gene (Ee or EE), it will be black or bay (or a black or bay based color, depending on what other modifiers are in the mix), but it needs TWO red genes (ee) to be "all red" (or a red-based color). Two dominant Extension genes (the "EE" genotype) creates what is commonly known as a "homozygous black". The term is confusing, because a horse can be "homozygous black" and not be an actual black horse at all, due to other genes it might have. It is more accurate to say the horse is homozygous for dominant Extension. 

Horses which have at least one "E" can produce both black and red pigment. Horses who are "ee" can only produce red pigment. Interestingly, from a historical standpoint, the chestnut or "ee" phenotype is a result of a later mutation of the original "E". The "Ee" and "EE" versions of Extension work along with another gene, Agouti, to create black, bay and brown.

Agouti (written as "A" and "a") is a dominant gene, meaning if a dominant A gene is present, it will affect the black based horse, making it bay or brown (at least one "E" plus at least one "A"). Agouti acts to restrict the black pigment to just the points of the horse- in other words, the mane, tail and lower legs. You could think of it as allowing the red pigment to show through on the body of the horse, in varying degrees. Chestnuts can carry agouti, but its effects won't show on them as they have no black hair to restrict to the points. They can, of course, pass it on to their offspring.

The recessive form of Agouti, "aa", works in conjunction with the dominant "E" Extension gene to create an all-black horse. Black horses cannot have the dominant, "A" form of agouti, because if they did, they'd be bay and not black.

To bring the above information into a couple of examples: a black x chestnut cross might produce a bay foal; this happened because the Agouti actually came from the chestnut parent, and the black pigmented base color came from the black parent. Two blacks cannot produce a bay, because there is no dominant "A" form of Agouti in the mix. Two blacks can produce a chestnut if neither is homozygous for dominant Extension (EE).

It was previously theorized that there were three different types of the dominant form of Agouti. "A", the Agouti which causes "regular" bay; "A+" for the "wild type" Agouti, which results in a light bay horse with very little black on the legs, usually just around the fetlocks; and "At" for brown, or what is sometimes called "seal brown", a nearly black horse with reddish areas on the muzzle and flanks. It is now believed that brown is not a separate type of Agouti, simply the darkest shade of bay. The genetic cause for wild bay (also called "low point bay") is currently unknown.

All of the other colors you see in horses are actually the result of other genes modifying the appearance of the three base colors: black, chestnut or bay/brown. The horse is still chestnut, black or bay/brown at its base color.

There is artwork depicting a medium shade of each color on each page of our Color Gallery. Be aware that the possible shades in each color may vary (lighter or darker) than what you see in the artwork; the photos used will illustrate those variations in shade. Also, keep in mind that the bay base horse will always be on the left, the chestnut based horse in the middle, and the black based horse on the right. This will help you remember what base color is "underneath" the various dilution genes and modifiers shown on this website.