Genetics Primer

Equine coat color genetics can be tricky, but this primer will hopefully give you a good foundation for learning.

Basic Terms

Step 1: Basecolor

Step 2: Agouti

Step 3: Dilution Genes

Step 4: Pattern Genes

Basic Terms

A gene is a code for a particular trait or feature. They control everything about an individual from appearance to metabolism and beyond. Genes are found in sets of two, with the individual genes in the set being called an allele.

A horse that is heterozygous has two different alleles. It can be said that he or she carries one copy of a particular gene. The horse will produce a foal carrying the gene 50% of the time when bred to a horse without the gene. Heterozygous cream dilutes are: palominos, buckskins, and smokey blacks.

A horse that is homozygous has two like alleles. It can be said that he or she carries two copies of a particular gene. The horse will produce a foal carrying the gene 100% of the time whether or not the horse it is bred to carries the gene. In order for a horse to be homozygous for ANY gene, both of the horse's parents must have the gene and pass it. Homozygous cream dilutes are: cremellos, perlinos, and smokey creams.

A Dominant gene is a gene that “dominates.” If a dominant gene is present, it will be expressed. It can not be hidden. Dominant genes are written as capital letters in genetic formulas. An example of a dominant gene is the black pigment gene, written as “E.”

A Recessive gene is a gene that can “hide.” In order for the gene to express itself, it must be in homozygous form (meaning both parents must pass the gene). Recessive genes are written as lowercase letters in genetic formulas. An example of a recessive gene is the red pigment gene, written as “e.”

Step 1: Basecolor

All equine coat colors start out with a basecolor. Basically, underneath all of the other genes, all horses are either red or black. Some people may refer to bay as a basecolor, but bay is really black + agouti.
 

Step 2: Modifiers

Color modifiers change the appearance of the base color. Color modifiers include Grey (progressive modifier that mixes white hairs with the coat color), Roan (modifier that mixes white hairs with the body color – true roans have solid heads and legs), and the most prevalent of the modifiers: the agouti.

The agouti is a modifier that regulates the distribution of black pigment. Put simply, it limits the black on a black horse to the points (ears, legs, mane, and tail). A red based horse (see "color recipes") can carry the agouti without showing it, as the agouti does not affect red pigment. However, a black horse can not carry the agouti without expressing it.

If your horse is "a" (actually shorthand for "aa") then he/she is homozygous recessive for the agouti, but it is easier to understand if I explain it as "NO agouti" (which is technically incorrect, but the easier to picture). Black horses are "aa." If a horse is "Aa", then he/she is heterozygous for the agouti and can throw horses with or without the agouti.

If a horse is "A" (shorthand for "AA"), the he/she is homozygous for the agouti and will NEVER throw black based horses without the agouti...that means NO blacks, smokey blacks, classic champagnes, blue roans, etc...any black-based foal will have the black limited to the points. So if you have a black mare and you want a foal who is "any color except black", then breed your mare to a stud who is homozygous for the agouti!

Step 3: Dilution Genes

Dilution genes are genes that dilute, or modify, existing pigment (color) in the horse's coat. Some examples of dilution genes are: the champagne gene, cream gene, the silver gene and dun gene. Each one is separate and effects the basecolor of the horse differently. A single horse may have several different dilution genes. See our composite champagne dilute pages under classifications.

Step 4: Pattern Genes

Pattern genes effect the placement of white throughout the horse’s coat. They are responsible for “spotted” horses. The pattern genes are the tobiano gene, the overo gene, and the sabino gene.