Basic Equine Color Genetics

by: Lynn Peterson

    I remember the first time I tried to send a jpg over e-mail. It felt like I was learning a total new language and thought I would NEVER get it. I compare this to when I decided to buy a cream Morgan and started to learn about color genetics. WOW how confusing. Now it seems so much easier and it is a never ending learning process. 

    Here is a very basic article on genetics I am not sure the author but it is a nice Ice breaker into the study.

The three basic colors of the horse. Chestnut, Bay, and Black

Chestnut	Bay	Black (with buckskin foal)

  The basic base color of horses, Chestnut, Bay, and Black, are found in two genetic Locus named Extension and Agouti

These two building blocks control whether a horse is chestnut, bay or black. They are separate of each other but work together.

The Extension Loci is a gene on a chromosome. Every horse has the same place on it's chromosomes for the Extension. Because every gene has a pair, Extension carries two alleles. They are either both recessive Labeled "ee", both dominate "EE", or they are one of each, a dominate and a recessive "Ee". 

The same goes for Agouti. It too has a specific place on a chromosone and has two alleles. Two recessive "aa" two dominate "AA" or one of each "Aa"

When an Extension carries 2 recessive alleles "ee" the horse is a Chestnut and the entire horse is red without any black.

It is most easy to think of "e" as a Chestnut gene.

It takes only one dominate gene to over power a recessive one. When one dominate allele is present along with one recessive "Ee" Chestnut is over powered by the dominate Extension allele and Agouti is called to action

Also if there are two dominate Extension alleles "EE" Chestnut is also turned off and Agouti is basically turned on.

If the Extension carries two recessive alleles "ee" we know it makes a horse a chestnut. What it also does is not allow black to be expressed on the horse's coloring. It Masks Agouti and does not allow it to be expressed. When one or two dominate Extention alleles are in the gene pair it turns off Chestnut and allows the expression of Agouti.

You can say "EE" is Homozygous for Agouti because there are two identical genes and these genes both allow Agouti or Black to be expressed on a horse's coloring.

You can say that "Ee" is heterozygous for Agouti because there is one "Chestnut" or recessive Extension gene and one dominate Extension gene. Since a dominate gene over powers or masks a recessive one. Agouti is allowed to be expressed.

What then is Agouti? Agouti is directly dependent on Extension for it's expression. If the horse is a chestnut then it's genes will be present but masked by the Extension. It is a bit confusing to think that two recessive genes can become dominate over another set but this is how Extension works. Two recessive "ee" alleles and Agouti is silent and not expressed. You can think of it as there but turned off.

However just one or two dominate Extension alleles and agouti is allowed to be expressed or turned on and chestnut is simply turned off.

Once Agouti is turned on by the Extension it may express black onto a horse's coloring either making the horse entirely black which is represented by two recessive Agouti alleles "aa". Or if the Agouti loci has one or two dominate alleles "Aa" or "AA" black is restricted to the points of the horse and it's mane and tail making the horse a Bay.

Black "aa" and Chestnut "ee" are similar in that they are both made up of two recessive Alleles. It only takes one dominate allele to mask a recessive allele. Therefore one dominate "A" paired with a recessive "a" will make a bay. As will two dominate alleles "AA"

It is most simple to refer to the recessive allele as Black "a" and the dominate allele as Bay "A" Bay would either be in it's homozygous form "AA" (two of the same allele) or Bay  in it's heterozygous form "Aa"( one  each of a recessive (black) masked by a dominate (bay) allele)

Lets take a moment to recap Extension and Agouti.

If we have an Extension of two recessive Alleles "ee" We know that the horse is a chestnut "ee". Chestnuts are always made up of two recessive alleles "ee" at the extension.

If Extension has one dominate allele and one recessive it is heterozygous for Agouti and masks the chestnut allele and allows Agouti to be expressed. "Ee" 

The same for if the Extension that has two dominate alleles "EE" . except now it is homozygous for agouti and agouti is allowed to be expressed.

Putting the genes together we can see how they interact to form the three basic colors of the horse. If Extension is Chestnut then remember that Agouti is masked. It may be any combination of bay or black alleles but they are masked turned off and not expressed on the horse.

A Chestnut horse's genotype would always be "ee" It's Agouti could be "aa" two  black, "Aa" one bay ,one black allele, "AA" two bay alleles.

"ee"+"aa" or "ee"+"Aa" or "ee"+"AA" All these genotypes are chestnut horses. Their Agouti is masked by the two recessive Extension Alleles.

If there is one or two dominate Extension alleles it turns off chestnut and on agouti. "Ee" or "EE"

Now the Agouti alleles is activated and will be expresses as the horse's coloring. We know from above that two recessive Agouti alleles are always Black "aa". One or two dominate Agouti alleles restricts the black to the points leaving a red body and the horse's coloring is now Bay. "Aa" or "AA"

A Bay horse's geneotype would look like these. All these horses are Bay

"Ee"+"Aa" or "Ee"+"AA" or "EE"+"Aa" or "EE"+"AA". The Extension has one or two dominate alleles turning off chestnut and allowing Agouti. The Agout alleles control whether the horse is black or bay. We know it takes two recessive Agouti Alleles to make Black "aa"

Therfore a Black horse's geneotype would be the folowing

Homozygous is a word we hear quite often but what does it really mean? In basic coat Color genetics Homozygous means two of the same gene.  Chestnut (ee) and Black (aa) are always homozygous because it takes two recessive genes to form that color and they can only give that gene to their foals.  It however does not always mean that that horse will ALWAYS throw that color. It depends upon the other mated horse's genetic color.

    Knowing what we do from above you should be able to tell what color a horse is from it's Genetic Loci. Here are the basic combinations of Extension and Agouti cover up the right half of the table and see if you can identify the color of the horse.

    You might be saying "WHY is all this important to the breeder?"  Basic understanding of color genetics help us as horse breeders understand what color our foals may or may not be. It also helps us to be able to market our stallions if they are homozygous and help us and our clients understand the possibilities of certain crosses. Let me take the time here to express that color should  be LOW on the list of attributes for breeding horses. It is however interesting to know this information for those of us who have colorful programs.

    Now that hopefully you understand the most basic formulas for color in horses lets put them together and make virtual foals. You can only be certain of what gene a horse will give their offspring if they are homozygous for that gene (have two of the same). Like the roll of the dice a horse will give only one of each of it's Extension and Agouti to it's foal.

    Say we have the following stallion with the genetic color formula -( "ee" + "aa"). We know that this horse is a chestnut because it has two recessive red genes and the extension is then turned on and agouti is turned off. This above stallion is also homozygous in both the extension and the agouti meaning he can only give an "e" and an "a" to his foals.

    If we breed this stallion to the following mare with this genetic genotype ( "EE" + "AA") which is a Bay mare - what can we get????? Because this mare is also homozygous for Extension and Agouti it is very simple to know what foals will be produced. There will be only one combination every single breeding and all the foals will be the same color. If we take one Extension and one Agouti from each parent and combine them we get the following foal. ("eE" + "aA") We know that from the Extension that it has turned on the Agouti and is NOT Chestnut. The Agouti says that the foal is Bay. This Chestnut stallion to this particular Bay mare will ALWAYS produce a Bay foal.

    If we take a stallion with the genetic makeup ("Ee + "Aa") and we breed it to a mare that has the genetic makeup of ("ee" + "AA") we will get the following possibilities. ("Ee") ("Aa") + ("ee") ("AA") which will produce the following:

("Ee + "AA") which is a Bay foal

("ee" + "AA") which is a Chestnut foal

("Ee" + "Aa") which is a Bay foal

("ee" + "Aa) which is a Chestnut foal

The following cross could only produce Chestnut or Bay but never a Black.

Look at the table below and see how many colors you can make from each cross. Remembering that the Extension is the switch for Chestnut or non Chestnut and that the stallion and mare give one of each genes randomly to their foals.

Q&A

Is is possible for a chestnut bred to a chestnut to produce a bay or black ? - NO, because a Chestnut is "ee", two chestnuts bred together will always give two "e"s to their foal meaning it will always be a chestnut.

Is is possible for a Chestnut to be a black producer? -  YES, A chestnut stallion for example could be hiding one or two recessive black Agouti "Aa" or "aa" which means if the Extension would have allowed the Agouti to be expressed the horse would have been bay or black. If this Chestnut stallion is bred to a none chestnut mare that also carries one or two recessive black agouti genes the foal has a chance of being black, bay or chestnut depending on the mare's complete color makeup. If the stallion is hiding "aa" it is a black based agouti horse and therefore may produce black foals at a higher rate when bred to non chestnut mares.

Can a horse be 100% homozygous for Bay and only produce bay horses no matter what color it is bred to?  -  YES, A homozygous Bay who has the genetic make-up of "EE"+"AA".  It can not produce Chestnut because it can only give an "E" to it's foal which automatically turns on Agouti and off chestnut. It also can only give an "A" to it's foal which does not allow black to be distributed throughout the entire body. Even if this horse is bred to a Chestnut with the genetic makeup of "ee"+"aa" the resulting foals will always be Bay. This type of Bay horse is the only genetic base color that is truly 100% homozygous meaning producing bay 100% of the time no matter what base color it is bred to.

Can a horse be 100% homozygous for Black and only produce black horses no matter what color it is bred to? - NO, Even if the Black horse is "EE"+"aa" meaning it can never produce a chestnut it still may produce a bay if bred to a bay mare because the bay mare carries one or two dominate Agouti "AA" or "Aa" meaning that it is possible that one "A" will be given to the foal and that would make the foal bay. 

Can a horse be 100% homozygous for Chestnut and only produce Chestnut horses no matter what color it is bred to? - NO, A Chestnut horse we know is always "ee" in it's Extension. It always gives one "e" to it's foal. But if the horse it is bred to has one or more dominate "E"'s meaning it is NOT a chestnut. The resulting foals may be bay or black depending on the Agouti genes present. A chestnut to a chestnut will ALWAYS 100% of the time produce a chestnut but a chestnut can not be homozygous when bred to non chestnut colors.

What about the Colorful horses????

    Colors such as Palomino, Dun, Buckskin, Grulla, Roan, Even Grey, are all over laid onto your three basic coat colors of Black Chestnut and Bay.

    Just for confusion's sake I will only discuss Cream Allele. Please think of Cream as an overlay that dilutes the base color. It does not change the basic Extension or Agouti just lightens red and does not effect black.

    A Palomino is nothing more then a Chestnut with one cream gene that lightens the red to gold and mane and tail to white. All the above still applys. A Buckskin for example is a Bay horse, it's genetic makeup could be "Ee"+"Aa" but because it also has one cream gene this gene effects the red in the body to gold but does not effect black meaning the points and mane and tail remain black.

    A Smoky Black is a Black horse either "Ee" +"aa" or "EE" + "aa" with one cream gene. Because Cream does not effect black, Smoky Blacks look like Black horses. Some Smoky Blacks are  lighter then True Blacks. It is thought that this horse would be a faded or lighter Black without the cream gene. Possibly with some other over laid gene effecting the black coat. There is so much that is still un known about contributing genes to the basic colors.

    There is some discussion about Brown being it's own base color. I personally do not believe this and believe that it is just a modified chestnut or bay but as time progresses more and more is known about the coloring of horses, it is always a progressive and ever changing learning experience.