Equine Color Genetics

Part 1 of a series.

Story and photos by Tracy Williams

Before delving into the numerous equine color combinations, it is important to understand basic genetics terminology – knowledge that will help you with every facet of breeding selection, not just this one. Here are the basic terms to remember:

1. Genes:
Genes are passed from generation to generation and determine virtually every characteristic of the horse’s physical makeup although they can also be influenced by the horse’s environment.

2. Chromosomes:
Chromosomes are packages of genes; they are the vehicles used to transfer genes from parent to offspring.

3. Locus:
A locus is the specific location of a gene on a chromosome.

4. Allele:
Each gene has two alternate states called alleles. The dominant allele masks the recessive, and the allele pairings determine the physical expression of that gene. The dominant allele is usually designated by a capital letter (i.e. “A”), and the recessive allele is usually designated by a lower-case letter (i.e. “a”).

5. Homozygous vs. Heterozygous:
If a horse has two dominant or two recessive alleles, it is said to be homozygous for the trait in question (i.e. “AA” or “aa”). If a horse has one of each, it is said to be heterozygous for the trait, and only the dominant form of the trait is expressed (i.e. “Aa” where only the “A” is expressed).

6. Genotype vs. Phenotype:
A genotype is the horse’s genetic code of various allele pairings. For example, “AA”, “Aa” and “aa” are all genotypes. The actual physical manifestation of the genetic code is called the phenotype – color, conformation, etc.

Color Development

While there are hundreds of color combinations in the horse world, we will begin our discussion with the three basic dark horse colors: bay, chestnut and black. Every other shade and nuance of shade can be traced back to these three. It is also important to note that background colors occur independently of white markings; white hairs are without any pigment at all and aren’t considered in determining a horse’s basic color. So, initially, disregard them; we’ll return there later.

Descriptions of horse color vary depending on geography, breed association and individual tastes and experience, but for simplicity’s sake, in this discussion we will consider bay, chestnut and black to be the following. Bay is the most frequently occurring horse color; it is characterized by a reddish brown body and black points (mane, tail, lower legs and ear rims). Chestnut is the second most frequent horse color, and it is distinguished by a reddish body and non-black points. Black horses are characterized by black bodies and black points.

These three colors are determined by two loci. One controls whether or not eumelanin is present, and the other controls the distribution of eumelanin. The Extension locus is the first. At this locus, the recessive state (“e”) prevents expression of eumelanin, the dark pigment. Therefore, a chestnut horse has two recessive extension alleles (“ee”) and only has dark pigment in the skin – not the haircoat. A horse that has one or both dominate alleles at this locus (“Ee” or “EE”) will be black or bay because eumelanin is allowed to extend into the haircoat, not just the skin.

The second locus involved is the Agouti locus, and the alleles at the Extension locus determine whether or not the alleles at the Agouti locus, are expressed. This gene controls the distribution of eumelanin. The dominant allele (“A”) allots dark color only in a horse’s points, not the rest of the body. The recessive allele (“a”) doesn’t restrict color, allowing black to extend throughout the body. Thus, a horse that is homozygous recessive at the Agouti locus (“aa”) will be uniformly black if the horse also has at least one dominant allele at the Extension locus (“aaEe” or “aaEE”). But a horse with one or two dominant alleles at the Agouti locus (“AA” or “Aa”) will be a bay – only black at the points with the body remaining red – if the horse has at least one dominant allele at the Extension locus (“AAEE”, “AaEE”, “AAEe” or “AaEe”).

Crossing Dark Horses

Now that you understand the inner workings behind even the most basic colors, you can see why it isn’t a simple process to obtain a certain shade. While there are some breeds that have become true-breeding for certain colors (i.e. Friesans with black or Cleveland Bays with bay), the rest of us play a genetic lottery to get a desired color. While crossing two black horses gives you a high probability of getting black offspring, you can also result in a chestnut foal. Two bays can give any of the three colors, although bay is the most likely. For more possible combinations refer to Diagram 1.

The diagram, however, isn’t foolproof. There are many other genes that interfere or further complicate these simple combinations. In further articles we will continue to explore genes that have resulted in the specific shade or pattern that identifies your beloved equine companion.