Horse Color Genetics: Red, Bay and Black

By Patty Wilber  

Horses come in only three basic colorsRed (=chestnut or sorrel), Bay, and Black.    

These colors are produced via 2 genes, the Eumelanin gene and the Agouti gene.  These two genes interact in a manner termed “epistasis”:  The Agouti gene, it turns out, can change the behavior of the Eumelanin gene.  

What are genes anyway?  They are segments of DNA (Deoxyribonucleic Acid, the molecule that is the genetic blue print of life) that code for a product.  In this case, protein.  The Eumelanin gene can control the production of black pigment, and each horse gets one Eumelanin version from mom and one Eumelanin version from dad.  So, each horse has two Eumelanin gene versions (technically, these versions are called “alleles”).  

The Agouti gene can modify the placement of the black pigment, if the horse has black pigment to place. Each horse also has two Agouti gene versions, one given by mom, and one given by dad.  (The egg and the sperm are kinda useful, as they each supply 1/2 of the DNA for the new horse!)

If we use “E” (black pigment is produced) and “e” (no black pigment is produced) to represent  the two versions of the Eumelanin gene, it follows that there are three possible combinations in any given horse.  

EE–each gene version results in the production of black pigment so the horse has a black base coat. (Although, the horse might not look  black if the black has been modifed…more on that next week.)  

Ee-one version of the gene results in black pigment production (E); the other one (e) does not.  Turns out that even 1/2 as much black pigment as the EE horse is enough that an Ee horse has a black base coat, too.  

ee-no black pigment produced, so the horse has a red base coat. If you breed a red horse to a red horse, guess what?  You get a red horse! Like Winston! Or Longshot! (Oh but his mom is a palomino–I will explain that next week, too!)  

Winston is red. ee.

For the Agouti gene we can use “A”-the black is restricted to the legs, ears, mane and tail.  “a”-no restriction of the black.   AA, Aa, and aa are the possibilities for any given horse.   

EEaa is a black base color horse.  Black pigment is produced (E) but it is not restricted (aa). (Eeaa is black too!)  

EEAA is a bay.  Black pigment is produced (E) but it is restricted to the mane, tail, ears and legs (A).  

Cometa is a bay (and Shelby is a dog)

 Interestingly, this is probably due to temperature–the black can only be produced on the cooler extremities of the horse.  Siamese cat points develop  in a similar way.  In fact, I read that if you put booties on a Siamese cat, and warm its feet up, you can make the feet go white–the pigment production gets turned off by the heat! It takes a while since it requires shedding of the one coat and replacement. In horses, I don’t think that works, though.  

What color are EEAa and EeAA and EeAa horses?  Answer at the end!  

eeAA and eeaa horses are RED, because the ee situation precludes the production of black pigment.  If there is no black pigment the horse can’t be black.  And, if there is no black pigment, the black cannot be restricted.  Thus, we are left with red.  What color is an eeAa horse?  

Thus, two genes, Eumelanin and Agouti, result in the production of the three main horse colors, red, bay, and black.  All other colors in horses result from modification of those three!

Next week: genetics of buckskin, palomino and the duns (dun, red dun, grulla)  



 EEAa and EeAA and EeAa horses are all bays.  E= black and A=restriction of the black.  

eeAa is a red horse.  ee= no black, so the black cannot be restricted, even though the A version of the Agouti gene is present.  

E i E i O = something Old McDonald says.

About BlogPatty

Here's the skinny: I have a thing for horses. They make sense to me. I have a small horse training business (it's a "boutique" training business, not because it's super fancy, but because the horses get a lot of personal attention). I also go by Dr. Wilber, and teach biology full-time at a Central New Mexico Community college.
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9 Responses to Horse Color Genetics: Red, Bay and Black

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  3. Leonore says:

    very interesting!! I will compare this in detail to the UC Davis horse coat color site, as I can’t get both to line up in my head on just one cup of coffee. I thought horses only came in two colors, and bay was a modification. live and learn!

    • Doranna says:

      Horse color stuff…so cool! I sometimes get a grasp on it, but it usually slips away. ;> I had a mare when I was younger (much), never did figure out what went into her color. Bay, but…not. She had weird color zones! And then went grey in a pattern I’ve also never seen.

  4. Sharon says:

    Wow! This is a lot to absorb – but – I think you have just cleared up a few things in my mind. You are a good teacher, and I’ll be studying this stuff for a while!

  5. Richard Hall says:

    But this seems to only explain solid color horses. What about black and white Appaloos’s and Paints. Actually Ei Ei O is closer to my level of intellect no matter how many cups of coffee I have.

  6. Patty says:

    Leonore–I debated about whether to say three base colors or two. I think Davis says two. I went with three because all horses are either red, black or bay and that is easy to see (well, pretty easy, except when you have a brown horse that might really be a red horse or a bay…but anyway.). I have to agree that bay is a modification of black though, so I would not argue with anyone who says that there are just two basic colors of horse, red or black. I was going to bring up the Davis site next week since you can send you horse’s hair in and they will tell you what genes the horse carries. Then you can do your own predicive crosses to see what kind of babies you might get from this that or the other stallion! The info I presented will match theirs exactly. Another interesting genetics person is Phil Sponenberg. He has done a lot with rare breed genetics (like the Spanish Barbs) as well as color.

    Thanks Sharon!

    Richard, you are absolutely correct. All other colors are modifications of the base. So a black and white horse is a black horse with some sort of white modifier–overo, tobiano and sabino are three genes that cause big patches of white over the body, in modification of the base coat. Appaloosa color genetics is especially complex and not super well understood..

  7. Sharon says:

    Sponenberg’s book is full of ugly horses! And it’s old-fashioned, although I know it is the “gold standard” Try Jeannette Gower’s “Horse Color Explained”. Much better!

  8. Dawn says:

    Can a cross with a EeAA and an Eeaa make a black foal?

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