Understanding the Basics
Dan Simmons

Color genetics is a fascinating subject in almost any species in my experience once you get into it and begin to get a handle on it.  In my prior critter life I raised and flew Birmingham Roller pigeons; amazing little aerial acrobats that did high speed spinning backward somersaults in the air above my home as I watched enthralled from below.  They had a lot of color possibilities in their genes that made breeding them for color in addition to good performance another interesting facet of the hobby.

Horses come in many colors as well and it has become popular to own and ride a horse of color for many people and increased their demand on the market.  In the current depressed market for horses, that can be a good thing, and understanding the basics at least of equine color genetics can be an important factor for breeders.  It can also be a fascinating subject for the average horse owner as well.

I do not purport to be an expert on it, but I have made a study of it and think I have a good understanding of the basics at least and am working on understanding the more complicated factors and modifiers that in some cases even the scientific experts don’t have a complete grasp on yet.  I know there are many who may be reading this that have as good or better a grasp on the subject as I, but I also have seen firsthand in my travels that there are also many who don’t.  There are many good resources in today’s cyber world on the internet that can aid you in learning more about this subject and I will name some of them as we go.

What many people aren’t aware of is that horses only come in two base colors, black and red; everything else our eyes perceive is a modification of those two base colors.  Every foal gets one base color gene from each of its parents to complete the pair each horse has; this is true of every gene pair in a horse’s DNA, or any species as far as I know, including us humans. 


Base Colors  -  Black and Red

So, as a starting point, a horse can have two black genes and will look black; or two red genes and look red; or one of each, black and red.  Of the two base colors, black is dominant over red, so a horse with one of each will look black.  This starting point is not considering any other factors or modifiers; we will build on the base from here.  In equine genetic code, a black gene is expressed as E and a red gene is expressed e; the dominant gene of a pair being the one in the capital letter.  The presence of two of the same genes for any pair, such as EE (black) or ee (red) is referred to as being homozygous for that trait.  Having one of each, Ee, is referred to as being heterozygous for that trait.


Bays and Browns

The next most common gene factor is a modifier of the black base coat color and is called an agouti gene.  The presence of this gene in the DNA chain is why there are fewer pure black horses running around than bays. The agouti gene comes in three different alleles or versions. A, a, and At.  An A agouti gene is dominant and will limit the production of eumelanin and turn all but the points of a black horse red; the points being the mane, parts of the head, tail, and lower legs, thus producing a bay horse. An a agouti is recessive and does not cause this effect.  An A agouti being dominant over an a, a horse can have a pair containing one of each, i.e. Aa and will still be a bay.   A red horse, already being red, an A agouti will have no effect on because it can only cause black to turn red on parts of a black horse.  The At agouti we’ll discuss in the next section.

So, let’s combine the agouti pair possibilities with the base color possibilities and see what we can get.

A homozygous black horse EE with two recessive agoutis aa: EEaa = a black horse, not a bay, a being the recessive agouti and having no affect on black.

A heterozygous black horse Ee with two recessive agoutis aa: Eeaa = still a black horse, black being dominant over red, and still not a bay with two recessive agoutis.

A homozygous black horse EE with two dominant agoutis AA: EEAA or one dominant agouti EEAa  = a bay horse, the dominant agouti changing the black to red except for the points on the horse.

A heterozygous black horse Ee with one or two dominant agoutis: EeAA or EeAa = still a bay horse as it expressed a black base coat with the one black gene dominant over the red base gene; and in the case of EeAA was made a bay by the dominant agouti gene pair and in the case of EeAa, the single dominant agouti has the same affect.

A red horse (always homozygous for red as if it had a black gene, it would not be red) ee with two dominant agouti genes AA: eeAA = a red horse.  A red horse is never directly affected by whatever combination of A or a agoutis it is carrying as it only affects the black gene and a red horse has no black gene to be affected. 

The At agouti is another story and it is less clear to me at this point, but it is what causes the brown color in a horse.  The At agouti is said to be more dominant than a recessive agouti a, but less dominant than an A agouti. That implies that if a black horse had an mix of A and At: AAt; it would be a bay horse and not a brown because the A is more dominant than the At and the brown would not show.  So, it seems to mean that a black horse with an agouti pair of AtAt or Ata would make the black horse brown instead of a bay.  The At gene that causes a brown horse is relatively rare compared to the other two agouti genes.

I will not go into such detail breaking down the color possibilities with the various gene groupings for the remaining colors I will talk about, but there are several web sites that will calculate them for you when you input what you do know.  In the Morgan world when you register your Morgan with the AMHA you of course have to submit hair from your horse as DNA samples and they will also do a color test for an additional discounted fee that can tell you what the above two gene results are; i.e. base coat and agouti genes.  For $10.00 more for each additional color test, they will also test other gene groupings for you in the process; relatively inexpensive if you would like to know those genes as well.


Creams - Palominos, Buckskins, Cremelos, Perlinos, Smoky Creams and Smoky Blacks

The Cream gene is one of the “dilute” genes.  The Cream allele is expressed as Cr and non-cream of the gene pair is expressed as C.  The cream gene dilutes the red color on a horse to a lighter shade.

A PALOMINO is a red horse for a base color or ee.  A single cream gene on a red horse dilutes the red to a yellow or gold color and turns the mane and tail almost white.

A CREMELO is a red horse with two cream genes, which further dilutes the red to almost a white color.

A BUCKSKIN is a bay with a single cream gene, which dilutes only the red on the horse and does not affect the black points.

A PERLINO is a buckskin with two cream genes which further dilutes the red to nearly white and dilutes the black points to an orange color.  Perlinos and Cremelos can be a little hard to distinguish and we have seen at least one miss-registered as a cremelo when it was actually a Perlino.  That was the case with the gaited Morgan filly below; the owner paid extra to test for the cream gene and got the results back it was a double cream gene and thought it was a Cremelo.  A base/agouti color test would have shown the horse was a black base with at least one agouti thus a buckskin under the double cream and therefore a perlino. The key visually is the mane and tail with the orange tint.

A SMOKY BLACK is a black horse, not a buckskin, that has one cream gene and can have very little effect if any on the coat color; sometimes it will show as a slightly ash color.  Before DNA testing there were at times controversy over parenthood when  a black horse threw a palomino or buckskin when neither parent was showing a cream dilution; we now know that the black horses were actually Smoky Blacks hiding a cream gene.

A SMOKY CREAM is a black horse with two cream genes and can be hard to differentiate from a cremelo, but they often have a light tan tint and can have darker tan or brown spots.

There are other dilute genes including the CHAMPAGNE and PEARL genes not known of in Morgans, and the SILVER DAPPLE gene which is found in Morgans.  Silver Dapple is only expressed in black based horses, and does not show on a red horse though they may carry and pass it on.


Shade, Sooty, and Mealy

There also other modifiers of base coats such as Shade, Sooty and Mealy.  SHADE affects the degree of darkness of the base color.  I’m sure most of us have seen bays for instance that are various degrees of darkness running from nearly black to a bright copper color.  In chestnuts they also can range from light red to dark livers or even a chocolate color.

SOOTY is still not well understood and still cannot be tested for.  It is seen in lighter colored horses such as palominos who have darker hairs and areas on their bodies.  As I mentioned above, silver is not expressed in a chestnut even if they carry it, but there are chestnuts, including our stallion Missouri’s Silver Rhythm shown below left, which have silver colored manes and tails.  This is thought to be flaxen chestnuts with the sooty gene making them look silver.  Interestingly, flaxen is not expressed in black based horses but is in red based horses.  Tit for tat I guess.  Rhythm’s dam is the flaxen chestnut, Mile High Donsanea.

MEALY or sometimes called PANGARE effects are seen as a yellow or pale areas on a horse’s lower belly, flanks, inner legs, behind the elbows, muzzle and over the eyes.  We had a mare, Castle Miss America, and have a mare from her, Ayla, shown below right, that have this gene.  If you look closely at the back of her hind legs you can see the lightening on the back of her legs, on her lower flanks, and the back of her front legs; it is more pronounced on her inner legs you can’t see in this picture.  She also has single white hairs throughout her liver chestnut body you can’t see here which are thought to be the effects of the SABINO gene.  Ayla has several modifiers at work; Shade darkening her to a liver; Sabino, and the Mealy or Pangare gene as well.  Interestingly, her sire was a black horse, Triple S Obsidian, and America, her dam, a bay; if you understand the basics, obviously both those horses were heterozygous for black and hiding a red gene.

Other Modifiers

There are other modifiers that are still not well understood such as ROAN, SABINO, APPALOOSA, and the paint effects of TOBIANO and OVERO.  Roan horses can have white hairs evenly interspersed over their body except the head.  Red based roan horses are often called “strawberry roans” and black based horses “blue roans”. PINTO horses come in two base patterns Overo and Tobiano though there are crosses called TOVEROS.  One interesting distinction is that Overo’s base coat color covers their back and the white does not cross the line between their withers and tail; on Tobiano, the white does cross over that line.  Sabino is not fully understood and is a fairly rare coloration that produces horses with areas of white rising high on the legs and on the belly and are irregularly shaped.  Appaloosa is another effect not fully understood either and Appaloosas can have a wide range of coloring or degree of spotting.  They do know the gene is incompletely dominant and effects are different depending on whether they have one or two of the genes.  Generally the homozygous, two genes horses seem to have fewer spots.

So, what color is your horse really?  Interesting stuff and can be important to know the basics at least if you are a breeder producing horses you hope to sell in a down market.  One of the best places I know to get a good handle on coat color, particularly in Morgans, though it holds true in any breed, is the web site www.morgancolors.com.  It breaks down the specific gene combinations with pictures of them all for reference.  I highly recommend it!

If you want to get your horse color tested, you can get the forms and pay online at www.vgl.ucdavis.edu/services/coatcolorhorse.php.

Happy Trails!