Preface  
Have you ever wondered why when breeding 2 chestnuts you always get a chestnut, but when breeding 2 bays you can get any of the basic colors (black, bay, chestnut)?

A basic understanding of the principals of genetics can help you to understand the mystery of horse colors.  

Genetics is not a simple concept to understand.  I am not a geneticist, but someone that started studying horse color many years ago because of our breeding program.  In many cases, to try and simplify the explanation, I do not use the vocabulary used by the scientists and geneticists.  I have intentionally avoided the use of terms such as locus and allele and instead used gene pair to describe the members of a chromosome.  

The Dominant Genes are much easier to understand than the combinations of black, bay and chestnut and I highly recommend that if you are looking for an introduction to basic genetics you first read the article Dominant Genes.

If you have any questions or notice anything in this article that is incorrect, please email me at judy@flightline.com. 

If after you read this article and would like to learn more I highly recommend the book "Equine Color Genetics" by D. Phillip Sponenberg, DVM, PhD.  There are also web sites that can help you understand specific colors. 

Genetics 101  
There are three basic horse colors, Bay, Black and Chestnut (sorrel).  All other colors are created by modifying these base color.  For example a palomino is a diluted sorrel and a buckskin is a diluted bay. 

Dilution Genes
Altering the base colors are dilution genes that include 
Cream Gene (Palomino, buckskin)
Silver Dapple gene
Champagne gene
Dun gene

Patterns of White
Adding white hairs to coat, either in patches (spots) or individually (grey or roan).
Grey
Roan
Tobiano (spotted)
Frame (overo spotting)
Sabino (overo spotting)
Splashed White (overo spotting)
Leopard Spotting (Appaloosa spotting)

A horse MUST have a base of either bay, black or chestnut - but can also have any combination of the dilution and white genes.  You could have a tobiano roan palomino or a horse that has the cream gene, the champagne gene and the silver dapple gene (would be rare, but possible).    

Bay, Black and Chestnut Horses

The two basic gene pairs that create bay, black and chestnut horses are called Agouti and Extension.  The Extension gene pair determines if a horse has black, the agouti gene pair determines if a horse has black on its body (black) or only on its points (bay).  For simplicity we will refer to the agouti as the "points" gene and the extension as the "black" gene.

The accepted representation for these gene pairs are:
Agouti (Points) - aa, Aa or AA
Extension (Black) - EE, Ee or ee  

The recessive genes are typically represented by a small letter ("a") and the dominant gene are represented by a capital letter ("A").

A horse that is Ee or EE will be black or bay, a horse that is ee will be chestnut. 

The "points" gene pair (agouti) will only express itself on a black horse.  Remember the "points" genes determine if the points will be black or the body will be black -- without the presence of black the "points" gene pair does nothing to change the horse color.  

So you can have any of the possible combinations of horses using just these 2 gene pairs:

Note that both "A" and "E" are dominant and only need 1 of the genes to express themselves.  The  "ee" and "aa" gene pairs are recessive and need both genes at that gene pair to be expressed.

Inheritance

Armed with the information on bay, black and chestnut horses we can now look at how offspring inherit color from their sire and dam and why some colors breed true and others do not.

Each parent contributes one gene from each gene pair to their offspring.  If the horse is homozygous at that gene pair the gene they contribute will always be the same.  If they are heterozygous at a gene pair they could contribute either the dominant or recessive gene.

Chestnut to Chestnut Breeding
In this example we are using a typical genotype for a chestnut horse, Aaee.  The genotype could also be AAee or aaee and the horse would still be chestnut.

Black to Black Breeding (Homozygous)

Black to Black Breeding (Heterozygous)
This would be a more typical breeding scenario

Bay to Bay Breeding

If you look at the genotypes for the dam and sire you will probably notice that the only difference is that they are Ee instead of ee.  This one small change makes a world of difference in what offspring the horse could produce.  A Bay horse could be of AAEE, AaEe, AAEe, or AaEE genotype.

That is a lot of genotypes and color combinations and each one means something different.  I will not go through this exercise for all colors, but it is important to get the concept of how many different color combinations can come from breeding 2 horses.  We are only working with 2 genes here and ended up with 9 different possible combinations.  Imagine the list when working with 5 or 6 of the color genes.  

Tables of Color Combinations for breeding chestnut/black, chestnut/bay and black/bay.  

If you have a basic understanding of why these foal colors come from the combinations listed, you have mastered the basic of horse color genetics.  

A few explanations: 
Reference Number 4 - when breeding a AAee Chestnut to a aaEE black you will always get a bay -- seems odd, but the "A" gene is contributed by the chestnut and the "E" gene contributed by the black -- any horse with both "A" and "E" will be a bay.

Reference Numbers 7,8,9,10,19 and 20  - Another example of only needing one "A" and one "E" to produce a bay.  Since the bay horse in this example is homozygous for both "A" and "E" the result will always be a bay, the chestnuts and blacks contributions are not relevant to the resulting visual color of the offspring (although they do contribute genes and will change the result of the actual genotype of the offspring and therefore what the offspring will produce when bred).

Determining Your Horses Genotype

This section is probably premature in that we have only discussed the 3 basic horse colors, but it is something that you can determine if you remove the dilution factors.  Palominos, flaxen sorrels and Gold Champagne are chestnuts with dilution.  Buckskins and amber champagnes are bays with dilution and smoky blacks and classic champagnes are black horses with dilution.

In most cases you can look at your horse and get a general idea of what color the horse is (not always true, but generally).  

You can probably determine visually if a horse is black, bay or chestnut .  Adding additional modifiers (cream, flaxen, champagne) can make this more confusing and less exact.  

You know your horses phenotype (visual appearance) but how do you determine your horses genotype.  This can be important when looking to breed your horse to produce a specific color foal. 

If your horse has produced any foals, this is a clue to his or her actual genotype.  You will need to know the color of the horse he or she was bred to and the color of the foal.  Also, if you know the color of the horses sire and dam, that can be helpful.

In these examples I will use ? when we are not sure of the gene at that gene pair.  

Chestnut based horses - "??ee"
Includes Chestnut, sorrel, palomino, cremello, gold champagne, flaxen sorrel, sorrel/white, etc.

We already know that a chestnut based horse is always going to be "ee" so we have that genotype.  What is at the "bay" gene pair is a mystery.  You may be able to determine some info from foals and ancestry.  

Ancestry -- If the chestnut horse had a black parent than he must carry at least one "a" - if both parents were black based then the horses genotype is "aaee".  If both parents are chestnut based it makes it much more difficult.  You can go back another generation to find any black or bay based horses to figure out the odds of "a" or "A" - but as soon as the chestnut base is introduced you have no way of knowing "for sure".  

For example your horses sire is chestnut, but his sire and dam were both black.   You could then determine that the horses sire was aaee and that he would have contributed the "a" to your horse and therefore you have "a?ee".  

If one of the parents was bay, the odds of your chestnut carrying "A" is increased, but since a bay can be "Aa" there is no guarantee that the bay passed the "A" to your horse.

Foals -- If you have had foals out of your chestnut horse you may be able to determine genotype that way.  

Foaling History:
1) Chestnut had a black when bred to a black or bay - genotype is "a?ee"
2) Chestnut had a bay when bred to a black - genotype is "A?ee"
3) Chestnut had a black when bred to a bay - genotype is "a?ee"

If your horse produces both 1 and 2 or your horse produces 2 and has a black parent you would know its genotype is "Aaee".  

Bay based horses - "A?E?"
Includes Bay, Buckskin, amber champagne, perlino, tri-color paint, etc.

We know that bays are "A?E?" - how do we fill in the blanks.  

Again if the sire or dam was black that determines the second "bay" gene and the horse must be "AaE?".  

Ancestry -- 
If one of the parents was chestnut then the second "black" gene would be "e".  (All chestnut horses are "ee").

If you have a bay out of a chestnut and a black, the genotype must be "AaEe".  

If the bay is out of 2 bays the horse could be "AaEe", "AAEE", "AAEe" or "AaEE".    

Foaling History:
Bay bred to any color and produced black --  "AaE?"
Bay bred to any color and produced chestnut -- "A?Ee"

Black based horses - "aaE?"
Includes Blacks, black/white, smoky black, smoky cream, classic champagne, etc.

Ancestry:
If one of the parents was chestnut based than the horse is "aaEe"

Foaling History:
Black bred to any color and produced chestnut -- "aaEe"

Determining Homozygous Genotypes
If after years of foaling, a horse has always produced a certain way you may be able to determine his genotype based on that.  This really only applies to stallions since most mares do not have enough foals to really even out of odds enough to make an intelligent guess on genotype.  

Some examples: 

If a bay or chestnut has been bred to many black mares and always produced bays, you may be able to determine that he is "AA".  

If a chestnut has never produced a bay based foal and has been bred to many blacks and bays you may be able to determine that he is "aaee".  

If a black or bay has 100% black and bay foals when bred to mares with a chestnut base, you might guess he is "EE".  

These are only guesses and you, and your customers, can be surprised at a later date if you make these assumptions.  You are much safer to assume heterozygous until the horse is either DNA tested or the number of foals that meet the criteria is at least in the double digits and you are probably safer to wait until you see 20 or 30.    

DNA Testing for absence of Red (BLACK)
There is a DNA test that will determine what is at the black gene.  "EE", "Ee" or "ee".  This enables you to determine if your horse is homozygous for the black gene.  This test works on both bay and black horses.  We know that a chestnut is "ee" so it would always come up as negative for black.  

If your black or bay horse has 2 parents with "E" (black or bay) it may be worthy of testing for "EE" to find out if your horse in homozygous for the black gene.

There are some valid reasons to use the test to determine between an "ee" horse and an "Ee" horse, these would be situations where you can not visually tell if the horse is black based -- silver dapples, smoky blacks that look like chestnuts and cream horses come to mind.