How To Read Your Horse's Test Results: Colors, Dilutes, and Patterns

Did you know that buckskin horses are technically bay with an added dilution gene? That golden coat is all thanks to coat color genetics! Like hair and eye color in humans, horses inherit specific genes from their parents that determine what color their coats, manes, tails, and even their eyes will be. Because color is a fascinating part of our horses’ genes, it makes sense that the Etalon Equine Genetics team is constantly working to deepen our understanding of known color genes and researching new variants. In addition to health and performance, all of our comprehensive DNA panels test for more than 40 colors and patterns for you to get to know your horse from the inside out. And the best part? We update our panels as we continue to learn more!

Whether you are looking to understand your horse’s unique combination of color genes or are just curious to learn more about the basics of equine coat colors, join us for this first installment of our “How to Read Your Horse’s DNA Results” series. We will be breaking down the basics of equine coat color genetics and how certain common color genes combine to create a horse’s unique coat color - or colors!

Base Coat Colors

Every horse has a base coat of either black or red (chestnut/sorrel) according to the horse’s main color gene, known as “Extension”. This is just as true of palominos, buckskins, grullos - you name it! That might sound impossible, but stick with us. Extension is the gene represented by “E” or “e” and it determines the horse’s base coat color expression in the absence of any modifiers. It is also sometimes referred to as “Red Factor” because it controls the production of red and black pigmentation.

There are two main variants, or versions, of Extension which are represented in two ways:

• E = Dominant variant which allows the horse to produce black pigmentation, which may cause the horse to appear black
• e = Recessive variant which prevents the production of black pigmentation, which may cause the horse to appear red in the absence of black

The DNA is the instruction manual as to how a particular horse will look, might perform, or what genetic diseases and abilities it may carry. The DNA (in horses) is contained in 32 pairs of chromosomes, and each individual inherits one chromosome out of each pair from its parents. Every organism from horses to humans inherits pairs of alleles, one allele from each parent. Each chromosome contains many regions that are responsible for individual traits or effects that can be referred to as a “gene”. Changes within each gene that alter function are called “variants”.

When your horse inherits two identical variants from their parents, the resulting combined gene is homozygous for that variant (as in “homozygous black” or E/E). If two different variants are inherited, the gene is heterozygous (as in “heterozygous black” or E/e). These combinations of variants/alleles determine our unique genotypes. In the case of color genetics, these alleles also influence phenotype. Simply put, a genotype is what an individual has for genes, and a phenotype is what we can observe or what is expressed such as their appearance, development, and behavior.

Dominant variants will produce that particular phenotype regardless of whether they are heterozygous or homozygous for that gene, hence the term dominant! In the case of Extension, the variant for Black “E” would be dominant and expressed over Red “e” (which is recessive). A single dominant variant can come from just one parent. For a recessive phenotype to occur, a red base coat for example, the individual would need to inherit two copies of the recessive variant, one from each parent. Because your horse inherits two variants, their results will read as “variant 1/variant 2”, as in “e/e” or “ee”.

Notice above that a capital letter represents a dominant variant and a lowercase letter is used for a recessive variant. This will be helpful as you read all of your horse’s results!

For Extension, this means your results will be one of the following possible combinations:

• E/E = Two Black (EE) variants. Base coat color appears black in the absence of modifiers. This horse has a 100% chance of passing “E” on to its offspring.
• E/e = One Black (E) and one Red (e) variant. Base coat color appears black in the absence of modifiers. This horse has a 50% chance of passing “E” or “e” on to its offspring.
• e/e = Two Red (ee) variants. Base coat color appears red in the absence of modifiers. This horse has a 100% chance of passing “e” on to its offspring.

The simple Punnett Square below gives you an easy tool for predicting genetic inheritance. The top is the stallion’s genetic variant set and the left is the dam’s. The squares on the inside represent four foal possibilities based on what they inherited from each parent. Each square represents a 25% chance of the foal having that combination. All four squares total a 100% chance of inheritance. In this case, the foal has a 25% chance of being homozygotes black (EE), a 50% chance of being heterozygous black (Ee), and a 25% chance of being red (ee).

Common Modifiers

Here is where things get interesting and we get into some of the “fun” colors! For the sake of simplicity, we will not get too far into the weeds in this article but know that there are a growing number of dilutions, modifiers, and genes for white markings that can further alter the color of a horse.

Agouti

The Agouti modifier (A) is what produces bay horses by restricting any black pigment to the outermost parts of the body. While Extension determines whether a horse has black pigment, Agouti restricts where the black pigment will be located. It is responsible for the remaining visible signature black points on the mane, tail, ear tips, and legs of bay horses. Agouti is an example of the genetic concept of “epistasis,” meaning that the effect of one gene is dependent on the effect of an independent gene. In the case of Agouti, this means that the modifier (A) can be present with both black and red base coats, but it only modifies the appearance of horses with black (E) base coats. This also means that for a horse to appear uniformly black, it must have at least one dominant variant at Extension (E/E or E/e) and be homozygous recessive for Agouti (a/a). Now let’s revisit our Punnett Square, this time with a few more variants. You can see how things can get crazy pretty quickly!

When combined with Extension, the Agouti modifier creates the following phenotypes:

• E/E or E/e + A/A or A/a (Black + Agouti) = Bay

• E/E or E/e + a/a (Black + No Agouti) = Black

• e/e + A/A or A/a (Red + Agouti) = Chestnut

• e/e + a/a (Red + No Agouti) = Chestnut