The Basics of Equine Color Genetics

Introduction: When I began this site back in 2002 (after a debate on a racing forum as to whether the Kentucky Derby and Preakness winner War Emblem was black or brown (he's brown)), very little information on horse color and the genetics behind it was available on the internet. Though I created the site just to explain color in Thoroughbreds, it quickly evolved into a comprehensive color site. Our knowledge about color genetics has grown by leaps and bounds since then, and while this site began with a very simplistic format, it has been necessary to update it with more complex information. I hope it is still easy to understand for those who are new to the subject. If you are not already familiar with basic Mendelian inheritance, please read this wiki page for more information. An understanding of dominant, recessive, and incomplete dominant genes is very useful when reading this site.

The Foundations: At the most basic genetic level, horses are either red or black. This is an over-simplification as I will explain below, but let's begin with the Extension locus as it seems to be the easiest way to segue into more complex matters. The Extension locus controls the formation of pigment in the hair, either black or red. Black (EE or Ee) is dominant to red (ee). Red (aka chestnut) is therefore recessive.That means that a horse carrying 2 black genes (EE) will be (homozygous) black; a horse carrying one black gene and one chestnut gene (Ee) will also be black (but heterozygous); and a horse carrying two chestnut genes (ee) will be chestnut (always homozygous). So if two heterozygous black horses are bred together (Ee +Ee), they have a 25% chance of producing a homozygous black (EE), a 50% chance of producing a heterozygous black (Ee), and a 25% chance of producing a chestnut. Two chestnuts bred together (ee + ee) can only produce chestnut.

That said, recent research indicates that the original, prehistoric color of modern equines was probably bay or possibly bay dun. A mutation of the Agouti locus, which acts to restrict the placement of black pigment, gave rise to black (completely unrestricted black pigment) and chestnut (lack of black pigment). Two alleles can occur at the Agouti locus: A (bay) or a (not bay, no restrictions on the coat). A is dominant while a is recessive. The factors that influence the shade of bay, from light to dark, are still being studied.

So the important thing to remember is that while it's easy to think of black and chestnut as being bases with all colors built on them, and to think of bay (or agouti) as one of the dilution genes, it's not strictly accurate (and I am guilty of having thought this way, too). Most of us learned to think about horse color this way, but recent research has shown bay came first and that black and chestnut are later mutations of bay. If you are interested in more in-depth reading on this subject, I highly recommend this post on Lesli Kathman's Equine Tapestry blog.

Przewalski's horses, also known as Takhi, exhibit what is believed to be the original (or close to ) primitive coloration for equines.

Chestnuts vary in shade from light golden red color to coppery red to dark liver. Some of the darkest liver chestnuts, often called "black chestnuts," are nearly indistinguishable from true black horses. Some chestnuts have flaxen manes and tails.

This is Affirmed, the 1978 Triple Crown winner, a light or golden chestnut.

This is top TB sire Rahy, a slightly darker golden chestnut.

This is the South African champion racehorse Horse Chestnut, a red chestnut.

This is top TB sire Giant's Causeway, a liver chestnut.

This is Merwin All A Breeze, a black chestnut (ee) Morgan. This shade is very rare.

This is Kerry Top Hat, a flaxen black chestnut Morgan.

This is a flaxen light chestnut.

This is a flaxen liver chestnut.
Black horses can also vary in shade---from blue-black to dusty black to sun-faded black. Not all black horses fade in the sun, but those that do generally resemble brown, dark bay, or even liver chestnut horses. The ends of their manes and tails often fade to a burnt reddish shade. The genetic factor governing non-fading black vs fading black has not yet been discovered.

Australian superstar Lonhro, a true, non-fading black TB.

A true black like Lonhro will not show any brown hairs on the muzzle.

This is K-One, a fading black Arabian gelding bred by Deal Arabians.
Note the lack of brown hairs on the muzzle.

This is Burn's Shadow Dancer, a very faded black TWH gelding.
As with the horse pictured at left, this horse also has no brown pigmented hairs on his muzzle
despite the sun-fading.

As discussed above, the alleles found at the Agouti locus control the expression of black pigment. They are as follows: A-agouti (meaning the horse is bay) and a-non agouti (meaning the horse remains black). (For quite some time, it was believed that more alleles existed, At (brown) and A+ (wild type bay), but this has now been debunked.)

This is Touch Gold, a light bay TB.

This is a red or blood bay.

This is Rambler's Renown, a dark bay Cleveland Bay. Note the lovely golden undertones and dappling. (Owned by IdleHour Stud)

This is Empire Maker, a dark bay TB.
The horse at left is also a bay, but the black on his legs is restricted to just his joints and pasterns. This is often called a wild type bay. It is thought to be a primitive coloration as it is often found in old breeds like the Fjord and Przewalski's Horse.

Brown horses are characterized by having a nearly black coat with lighter brown hairs on their muzzles, flanks, inner forearms, and inner thighs. Seattle Slew is an excellent example of this color. (Photos by Anne Eberhardt) This color is genetically the same as bay, but what determines such a dark shade is not yet known.

On to the Dilution Genes