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, most of our comprehensive DNA packages and our Color Panel test for more than 20 colors and patterns for you to get to know your horse from the inside out. And the best part? We update our packages and 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 homozygous 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

Cream

The Cream dilution (CR) is one of many variants of a gene that can reduce the overall amount of pigmentation, thus diluting the color of the horse. The CR variant is an example of incomplete dominance where a single copy (CR/n) behaves differently than two copies (CR/CR). Heterozygous creams (CR/n) have red coats diluted to gold with white manes and tails, with black coats appearing mostly unaffected. However, horses with homozygous cream variants (CR/CR) show an extreme dilution of the hair, skin, and eyes of any color, with black-based horses tending to retain slightly more pigment than red-based horses.

In combination with the Extension gene and the Agouti modifier, the cream dilution creates the following phenotypes:

• E/E or E/e + a/a + CR/n (Black + 1 Cream) = Smoky Black

• E/E or E/e + a/a + CR/CR (Black + 2 Cream) = Smoky Cream

• E/E or E/e + A/A or A/a + CR/n (Bay + 1 Cream) = Buckskin

• E/E or E/e + A/A or A/a + CR/CR (Bay + 2 Cream) = Perlino

• e/e + a/a + CR/n (Chestnut + 1 Cream) = Palomino

• e/e + a/a + CR/CR (Chestnut + 2 Cream) = Cremello

Dun & Primitive Markings

Dun (D), which is a dominant dilution gene, is the ancestral coat color of equids. However, the lack of dun dilution is more common in most domestic horse breeds. Both homozygous (D/D) and heterozygous (D/nd1 or D/nd2) horses display the same effects on the coat color. The characteristic dilution is the result of pigments clustering asymmetrically to one side of the hair shaft. The dun dilution affects both pigment types equally (unlike the cream dilution), however, the points often are darker than the body. Dun horses also display “primitive markings,” including a fully pigmented dorsal stripe, leg barring, shoulder stripes, face mask, face cob webbing, ear stripes, and/or lighter hairs along the mane and tail, known as “frosting.” These primitive markings are often more prominent on homozygous dun (D/D) horses.

Two known variants of this color gene result in non-dun phenotypes. Horses with non-dun 1 (nd1/nd1 or nd1/nd2) lack the distinct dilution seen in dun horses, but may still display some primitive markings. Horses with one copy of non-dun 1 often show the dorsal stripe indicating that it is likely an incomplete dominant variant rather than recessive with the possibility of being epistatic. Horses with non-dun 2 (nd2/nd2) lack both the distinct dilution seen in dun horses as well as the primitive markings.

In combination with the Extension gene and the Agouti modifier, the dun dilution creates the following phenotypes:

• E/E or E/e + a/a + D/D or D/nd1 or D/nd2 (Black + Dun) = Grullo or Grulla

• E/E or E/e + a/a + nd1/nd1 or nd1/nd2 (Black + Non-Dun 1) = Black with primitive markings

• E/E or E/e + a/a + nd2/nd2 (Black + Non-Dun 2) = Black

• E/E or E/e + A/A or A/a + D/D or D/nd1 or D/nd2 (Bay + Dun) = Bay Dun

• E/E or E/e + A/A or A/a + nd1/nd1 or nd1/nd2 (Bay + Non-Dun 1) = Bay with primitive markings

• E/E or E/e + A/A or A/a + nd2/nd2 (Bay + Non-Dun 2) = Bay

• e/e + a/a + D/D or D/nd1 or D/nd2 (Chestnut + Dun) = Red Dun

• e/e + a/a + nd1/nd1 or nd1/nd2 (Chestnut + Non-Dun 1) = Chestnut with primitive markings

• e/e + a/a + nd2/nd2 (Chestnut + Non-Dun 2) = Chestnut

If you are curious about even more coat color modifiers, dilutions, and patterns, check out a more extensive (but not exhaustive!) list that we have compiled here.

As you can see; the concept of coat color genetics is pretty simple, just build the layers. However, the math starts to get crazy quickly. We thought about putting the corresponding Punnett Squares here for the Dun and Cream layers, but those graphics would not even fit on the page! So now what? Enter technology for people who love horses but would rather ride than run math models! Read on, friends…

The Relationship Between Color and Health

As fun as it is talking about coat color, we would be remiss not to discuss the relationship between some color genes and equine health. While plenty of the known color genes appear to have no negative effects on a horse’s health, there are a few that we know do such as grey and lethal white overo.

Grey

Grey (G) is another coat color modifier that results in the progressive loss of pigmentation throughout the coat. Truly grey horses are born a darker color displaying their phenotype before their coat “greys out” and begin to display more white hairs with each shedding. Their skin remains dark throughout their lives which is what distinguishes them from horses who have significant white spotting and pink skin. Grey is a dominant trait, so a horse only needs to inherit one copy for their coat to display it. While the rate of greying varies, some research has shown homozygous grey (G/G) horses will grey out faster than heterozygous grey horses (G/n).¹

There are several other pigmentation traits associated with greying. While some horses lose pigmentation fairly uniformly, others form light circles with dark borders (dapple grey) or retain dark speckling on a lighter background (flea-bitten grey). Grey is also associated with vitiligo, which is a patchy loss of pigmentation of the skin. Homozygous horses (G/G) tend to show less speckling and are more likely to be affected by vitiligo than heterozygotes (G/n).

Where grey gets tricky, however, is in its known association with the development of melanomas. Research has indicated that melanomas occur in approximately 70-80% of grey horses over the age of 15.² ³ Most grey melanomas are slow-growing, benign tumors that do not significantly impact the health of the horse. However, some melanomas become malignant, and in rare cases, are malignant from the onset. Further research has indicated that 66% of grey melanomas will become malignant. Studies have shown that horses who have both the “G” allele and at least one “a” allele of Agouti are associated with a higher melanoma incidence.¹ However, as age is also associated with melanoma incidence, it may be better to think of homozygous greys (G/G) and black-based horses (a/a) as more likely to develop melanomas at a younger age. Other minor genetic factors affect the incidence and severity of melanomas, although the exact genetic loci are not known at this time.

Lethal White Overo (Frame Overo)

Lethal white overo (LWO), sometimes referred to as frame overo, is another color gene with serious health implications. The white spotting pattern associated with lethal white overo is thanks to a variant of the EDNRB gene, which is vital for normal development. It is most often associated with paint horses but has also been found in other stock-type breeds as well as miniature horses and other breeds. Color-wise LWO is an example of incomplete dominance meaning horses with one copy have a different phenotype, or look different, than horses with two copies.

Homozygous lethal white horses (LWO/LWO) are born completely white and with underdeveloped intestinal tracts. They are unable to properly digest food or defecate, leading to gastrointestinal pain and colic typically within 12 hours of birth. As a sad result, affected foals often die within just a few days of birth due to bowel rupture or bacterial infection. There is no treatment available for these foals and for that reason, they are often humanely euthanized. Health-wise LWO is a recessive health trait, meaning two copies need to be inherited for this serious health condition to occur.

Heterozygous horses (LWO/n) tend to have patches of white-bordered (“framed”) by normal pigmentation, often paired with blue eyes. Some heterozygous LWO horses do not display a white spotting pattern at all but can still pass the gene onto their foals. If you were to breed two horses that were both carriers of LWO (LWO/n) but did not look like it, there is still a 25% chance of producing a homozygous LWO (LWO/LWO) foal. This is why genetic testing is so crucial for responsible breeding regardless of what your horse looks like on the outside.

Color Me Curious: Play with color using our interactive tools!

If you can’t get enough of the science of coat color and want to see the genetics in action, check out our fun, interactive tools! You can use our Build-A-Horse tool to pair real stallions and mares in our database, to create your dream foal based on their genetics. Check it out in the Etalon dashboard today!

If you’re not necessarily into playing matchmaker but are still interested in seeing color genes work their magic, you can also play around with our Horse Coat Color Simulator Tool. The coat color simulator is perfect for visualizing how various color genes interact in real time!

From bays and chestnuts to duns and palominos, we now know that the gene combinations behind a horse’s coat are much more than just black and red - the story is in the nuances of the various color modifiers and dilutions that work together to create a living, breathing, equine masterpiece. Understanding and interpreting the many color genes in horses can be a complex topic, but even a basic understanding of the base coat colors and their effects can help unlock the mysteries of your own horse's color.

As we learn more about which genes are responsible for each unique color combination, we can continue to deepen our understanding of our horses and what makes them so special. Our journey into equine coat color genetics is just beginning, but discovering and exploring the wonderful diversity of our horses’ genetic makeup is a trip worth taking. Even if you think you know what color your horse is, you might be surprised by their individual results. So what are you waiting for? Order your panel today, participate in the research and discovery, and get to know your horse down to the DNA!

References

¹ Rosengren Pielberg, G., Golovko, A., Sundström, E., Curik, I., Lennartsson, J., Seltenhammer, M. H., Druml, T., Binns, M., Fitzsimmons, C., Lindgren, G., Sandberg, K., Baumung, R., Vetterlein, M., Strömberg, S., Grabherr, M., Wade, C., Lindblad-Toh, K., Pontén, F., Heldin, C. H., Sölkner, J., … Andersson, L. (2008). A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse. Nature genetics, 40(8), 1004–1009. https://doi.org/10.1038/ng.185

² Fleury, C., Bérard, F., Leblond, A., Faure, C., Ganem, N., & Thomas, L. (2000). The Study of Cutaneous Melanomas in Camargue-Type Gray-Skinned Horses (2): Epidemiological Survey. Pigment Cell Research, 13(1), 47-51. https://doi.org/10.1034/j.1600-0749.2000.130109.x

³ Sutton, R. H., & Coleman, G. T. (1997). Melanoma and the Graying horse. RIRDC Research Paper Series, 55, 1-27.