We need to know some very basic genetics first:

Genes - a segment of genetic material that codes for a particular trait.

Chromosomes - a string of genes

Locus - The genes each have a specific location on a specific chromosome. This location is called a Locus.

Allele - A gene can come in more than one form, which is what cause animals to have different traits, for example, blue eyes or brown. These different forms of any gene are called Alleles. Since we know that there are 2 loci available (one on each chromosome) for any given trait, each animal has 2 genes for each trait. One of these is from the mother and one will come from the father.

These genes will either determine:

Color loci we will consider here are A, C. and E.

Pattern loci we will consider are Dn, Rn and To.

The A Locus (or "Agouti Locus")

This locus controls the relative distribution of black on horses that can produce black pigment.

The dominant allele at this locus, A⁺, causes black to be restricted to the points (i.e., the mane, tail, and lower legs). This is the most natural color for a horse to be.

The recessive allele, A^a, allows the black pigment to be produced over the whole body and results in a black horse.

So, possibilities at this locus are:

A+A+	A+Aa	Aa Aa
bay	bay (because A+ is the dominant allele)	black

If we breed a homozygous bay horse to anything else (considering only the A locus), we always get a bay horse, because always has the A⁺ allele, and that one is dominant.

If we breed 2 heterozygous bay horses to each other, we come out with:

Please notice that we can’t tell a homozygote from a heterozygote because A⁺ is dominant over Aa and both genetic types (or genotypes) appear as bay.

The E Locus (or "Extension Locus")

At the E locus, the natural form of the gene (or "wild type"), expressed as E⁺, allows black pigment to be produced in the horse. If a horse has at least one E⁺ at the E locus, the appearance will be what we have already determined by looking at the A locus.

The recessive form of the E gene, E^e, prevents black pigment from being formed in the coat, and allows only the red.

Thus, no matter what we have at the A locus, if a horse is homozygotic at the E locus for the recessive allele E^e, we will have a chestnut horse.

So, if we breed 2 chestnuts, we must always get chestnut, because E^e is recessive, and both parents are E^eE^e and can give only the E^e allele to offspring.

If we breed a bay and a chestnut, the result depends on whether the bay is E⁺E^e or E⁺E⁺.

If the bay is E⁺E⁺, the baby gets E⁺ from the bay parent and E^e from the chestnut parent. All foals from this cross are E⁺E^e and are bays.

But if the bay parent carries the recessive E^e, and is E⁺E^e, half the time the foal will get E⁺ from this parent and will be E⁺E^e, or bay and half the time will get the hidden recessive E^e from this bay and, along with the E^e from the chestnut, carries only E^eE^e. So we have a chestnut foal.

So by looking at foals produced, we can often tell if a bay has 2 dominant genes at the E locus (E⁺) or only one. If a bay parent produces a chestnut foal, you know it carries the hidden recessive E^e.

The C Locus (or "Color Locus")

The C locus determines whether full color is produced, partial color, or no color.

It is a large series of alleles. This is the locus that controls shading in Siamese cats and shaded rabbits.

There are three alleles in this series that interest us:

C⁺ is the most dominant allele. Animals with either one C⁺ or two, C⁺C⁺, express full color.

C^c is the albino gene. This gene does not allow any color at all at all to be expressed. While the albino gene is found in many mammals, it is not known to exist in the horse. There are no albino horses.

C^Cr is the cremello gene. This one interests us a lot. If a horse has one C^Cr gene, most of the red pigment is pulled out of the coat.

Thus, a chestnut, which is all red, becomes a palomino. A bay, which is red in the body and black in the points, loses most of the red body color to become a buckskin.

If a horse gets two C^Cr genes, one form each parent, most of the color will be reduced to an off-white, or cremello. On a bay, not only does the body color lighten, but the point color as well. Sometimes a bay cremello (commonly called a smoky crème) will have just a touch of pigment left in the tail, but often they are as light as a chestnut cremello, and you can’t tell the difference.

Those are the main equine color genes. There are a lot of modifier genes that cause differences in individuals with these colors, and there are a few alleles I have not mentioned, such as the wild bay allele and dominant black.

Pattern genes are simply genes that cause a pattern to be superimposed on the base color as determined by the A, E, and C loci.

Common Pattern Genes on Assateague

Dun - Often called "linebacked duns", this pattern is caused by a dominant allele, Dn⁺. It can be superimposed on any color and causes a stripe down the back and sometimes on the knees and hocks. It’s easy to spot this gene by looking for the stripe.

Roan - Rn^Rn - a dominant allele causing white hairs to be scattered through the body.

Tobiano paint - To^T is another dominant allele. One dose of To^T causes the tobiano paint pattern.. So, you can get a solid horse from breeding 2 paints if each is carrying the recessive solid allele. But you cannot get a paint from 2 solids, because the paint gene is dominant, and you will see it if it is present.

Pattern genes not on Assateague

Gray - G^G - causes increasing numbers of white hairs to appear in the coat until the animal appears to be nearly white. At some stages, can be confused with roan.

Overo paint - paint patterns are usually in an oval pattern - white areas do not usually cross the back. There are several distinct types of overo patterns, caused by genes at at least 3 separate loci. Overo paints are a lot more complex than tobianos, which are due to a simple dominant allele at the To locus.