The ABC's of Coat Color Genetics

The True Color of Genes



A good horse is a good horse regardless of his color."


Yes, scientifically color has nothing to do with the heart of a race horse or whether a horse can "cow", jump fences, run barrels or do any other specific job. A correlation has never been found between color and performance ability.

Yet, color can be a big drawing card when a horse is for sale. It can definitely make a difference in the amount of attention a horse gets in the show ring.

Most horsemen seem to have a color preference. Some prefer palominos, others like grays, or buckskins, or tobianos. . . For every color there is a group of people who feel that their color is the most beautiful expression of the body of the horse.

Perhaps it is because of our human preferences that coat color genetics is one of the few areas of equine genetics that scientists have been able to develop sophisticated theories on how specific genes determine the color of a horse's hair.

However, it is important to realize that much of the theory of coat color genetics is just that a theory.  Currently  The Veterinary Genetics Laboratory  at the University of California at Davis is at the forefront of developing tests which identify the presence of specific genes related to coat color.                                     

At this time,  five genes can be confirmed in the laboratory - the tobiano gene (T - sometimes referred to as To), the recessive form of a gene that creates a red horse (e), a specific overo gene that can be lethal (commonly referred to as  O),  the cream dilution gene that creates some palominos and buckskins  (CR) and the gene that turns black to bay - the A gene.

The action of the remaining color genes is purely hypothetical. Because of this, theories may change as more and more tests become available to identify specific genes.

Identifying coat colors can also be cause for confusion. There is a tremendous range of shades within a color and different types of colors without any recognized names. There are also coat colors that appear to be identical, but are under the influence of different genes.

Breed associations have also contributed to some of the confusion.

Take, for example, the gray gene. Technically, whenever the gray gene is present in the dominant form, the horse is a gray regardless of its base coat color. Any color horse (with the exception of the true white) can turn gray.

However, The Jockey Club registers their horses under a different system. If a red horse has white hairs in its coat, The Jockey Club refers to it as a roan –regardless of gene creating the coat. According to The Jockey Club, grays are dark horses which are graying.

The Jockey Club is not alone. Most breed associations do not register coat colors according to the current theory of coat color genetics.

And to make it even more confusing, these organizations do change their color categories on their registration forms.

For example, The American Quarter Horse Association changed the description of a "buckskin". In the past a buckskin was any canvas colored horse with black points. It could have zebra markings and a line-back and still have been a buckskin.

Today, all line-backed horses with zebra markings are referred to as duns - that is, unless they are sorrel or chestnut duns. These are called red duns while black duns are called grullas.




The roan horse recognized by the APHA and the AQHA can be another source of confusion.

The AQHA has two choices for roans - the blue roan and the red roan - the category which lumps together bay roans and sorrel/chestnut roans.  That is, until 2002 when the registration form added a separate category for bay roans. 

Up until recently, roan Paint Horses were registered according to the same guidelines used by the American Quarter Horse Association. However in 2000, the APHA decided to divide the roans into the three basic colors:


                        1. The blue roan

                        2. The bay roan

                         3. The red roan






In spite of having to muddle through the confusing labels used by the various breed organizations, it is possible to stack the deck in order to increase the probability of producing a specific colored offspring - if you understand the underlying genes which create the colors.

But, first, before delving into the the genes that control coat color genetics, there are three concepts that you need to understand:

                        Genes and how they are passed to the next generation

                        How a matched pair of genes basically relate to each other

                        How to predict the possible gene combinations

Lets get started.


Genes and chromosomes

Genes are the basic units of inheritance.

Genes are linked together to form a chromosome similar to the way pearls are threaded together to make a strand.

Chromosomes exist in pairs. Each gene on the chromosome has a mate or "allele" in exactly the same place or "loci" on the chromosome's matched pair.

Each particular species has a specific number of chromosomes. For example a horse has 32 pairs of chromosomes. A donkey has 31 chromosomes pairs.

Basically each pair of genes codes for a specific job. A pair of genes can control something as obvious as whether or not a cow will have horns or be as subtle as coding for a specific portion of a biological molecule.

During the cell division when one cell divides into either two eggs or two sperm cells, only one member of each chromosome pair goes into each new cell. This provides every sperm and egg with only one copy of each gene.

For example suppose a stallion has at one gene location along the chromosome, genes designated as E and e. When that cell divides into two sperm cells, one resulting sperm cell will get the chromosome with the e and the other resulting sperm cell will get the other chromosome with the "E".



This same process takes place in the mare as she produced eggs.

Upon fertilization the single chromosomes find their corresponding mate and pair back up. The resulting individual again has two genes at each location – one from its dam and one from its sire.

To help keep track of the genes whose function is thought to have been identified, geneticists assigned a letter or two of the alphabet to each pair.  For some of the newly identified genes there may still more than one common abbreviation.   For example, the cremello gene which creates palominos and buckskins may be referred to as CR or C  with a cr superscript.

In this course, we are going to use the simplest codes but don't get tunnel vision about the gene abbreviations.  It is inevitable that some of the notations will change as geneticists learn more about the genes that control coat color.

Here is a list of genes that we will be discussing and the gene abbreviations that we will use.

Coat Color Genetic Codes

Coat Color

























Gene Relationships

Gene interactions can be complex, confusing, and elusive. Fortunately, some genes adhere to a relationship based on simple dominance.

Genes that interact under the terms of single dominance exist in only two forms.

    • One form of the gene is dominant meaning that its form will be expressed. Capital letters usually are used to indicate the presence of the dominate gene.
    • The recessive form of the gene is submissive to the dominant form. lower case letters indicate recessive genes

When there are just TWO possible expressions for a specific gene – either dominant or recessive – there are only three possible ways this matched pair can exist.

                                                1.  Both genes are in the dominant form

                                                2.  Both genes are in the recessive form

                                                3.  One member of the pair is in the dominant form.  The other is in the recessive form.

Homozygous and heterozygous are words used to identify which gene combination is present. These words sound difficult but the roots of the words are common in our language – hetero meaning different, homo meaning the same..

Putting together the concept of dominant vs recessive and homozygous vs heterozygous provides us with the language used by geneticists to describe gene relationships.

When a gene pair is said to be Homozygous Dominant, it means that the genes are in the dominant form as indicated by capital letters, for example, AA. The color determination is under the control of the dominant gene and all offspring created from this individual will receive a copy of this dominant gene.

When both copies of the genes are in the recessive form, the term that is used is Homozygous Recessive,.  Foals who have a parent that is homozygous recessive for a particular gene must receive one copy of that recessive gene.


A sorrel horse is homozygous recessive - ee.      

When the matched pair exist in the dominant/recessive relationship, the relationship is referred to as Heterozygous. The dominant form is in control of the expression and all offspring have a 50-50 chance of inheriting either the dominant or the recessive gene.


A black horse may be either homozygous dominant (EE) or heterozygous (Ee).  Either way the dominant gene will be expressed.

Predicting Gene Combinations

The last concept to be mastered before we begin our discussion of coat color genetics is how to predict the possible gene combinations that could occur from the mating of two horses. The Punnett Square is a tool that simplifies the process.

To use the Punnett Square

            Draw a square – actually a rectangle with 2 columns –one for each of the gene pairs contributed by the stallion and two rows – one for each of the gene pairs contributed by the mare.












Across the top, place each one of the genes contributed by the stallion into a separate column. For this example, let’s assume the stallion is homozygous recessive or aa.











Down the left side, place each one of the possible genes contributed by the mare into a separate row. Let’s assume this mare is heterozygous or Aa












To create a mating, enter the gene notation from the top of column and enter it into the blank boxes below.












Now enter the gene notation at the side of each row into each box in the row












The resulting table indicates the gene combinations possible from the mating of this stallion to this mare. Each box represent a 25% chance.

In this example, foals from this cross have a 50% chance of getting the Aa combination and a 50% chance of aa.

Now that we have a very basic understanding about genetics, let’s begin with two genes – the A and the E which determine the basic coat color of all horses - black, bay and chestnut. The next lesson…..