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How to Read Genetic Testing Results: A Complete Guide to Understanding Your Horse’s Color

So you've gene tested your horse and gotten the results, but what do they mean? The color name — also called phenotype — makes sense, but what about that string of letters? That's your horse's genotype, the actual genetic code for the coat color of your horse, and here we're going to break it all down and explain how to read it.

GeneticTestingResults.jpg

This is one of the most complex genotypes that can be created in the game. If you’re just starting out, I’m sure it looks pretty confusing, but by the end of this tutorial, every part of it will make perfect sense. You may eventually find you get a quicker mental picture of the genetics of your horse by looking at the genotype rather than the phenotype. So let’s get started and break it all down.

The Base Coat

Extension & Agouti

Extention&Agouti.jpg

All horses have these four letters in their genotypes and they are the base of every other possible horse color. So let's zoom in for a moment on these.

E represents Extension, which is responsible for giving your horse black pigment. All black horses have an uppercase E in their genotype, and only one uppercase E is required for your horse to have black pigment. If your horse has two lowercase e's, it will have no black pigment and its base coat will be entirely red pigment — most likely chestnut if no other genetic factors are at work. Since black pigment is darker than red, when it is present at all, it completely masks the red pigment "beneath."

Uppercase E gives your horse black pigment.

A represents Agouti, which restricts the amount of black pigment expressed on your horse's coat. Agouti works by removing black pigment from the base coat, showing the red beneath. An uppercase A removes some black pigment from your horse's body, making it a bay (red with black points). An upcoming game update to Agouti will make a second A remove even more black pigment than a single A. All bay horses have an uppercase A in their genotype. If the bay horse had two lowercase a's instead, it would be a black horse. Agouti has no effect on chestnut horses, since chestnut horses have no black pigment to be affected.

Uppercase A restricts the expression of black pigment, if present.

baseCoats.jpg

Horses with E, whether or not they have A, are known as “black based.” Horses that are e/e are known as “red based.” Almost all other genes will work by causing some modifying effect on red or black or both types of pigment. When a horse has both an uppercase and lowercase letter, it makes no difference to the phenotype which comes first. A/a will look the same as a/A. The only thing to keep in mind about the order that the first letter was inherited from the sire and the second was inherited from the dam.

If you see an A* in your horse's genotype, treat it as though it were A. It will soon be removed as part of an ongoing update to Agouti to make it better represent the most up-to-date scientific research on horse color genetics.

But what does it really mean for a letter to be uppercase or lowercase? A lowercase letter doesn't necessarily mean that your horse doesn't have the gene, it indicates allele dominance. So, before we go further into the rest of the letters in the genotype above, let’s take a moment to explain some basic genetics terms.

Dominant & Recessive Alleles: A Brief Explanation

Genes & Alleles

Each pair of letters in a horse’s genotype represents a gene and each letter within each pair represents an allele for that gene. An allele is a version of the gene, i.e. Extension is the gene and E and e are the two versions (alleles) it can come in. Some genes have more than two possible alleles, but only two can be carried by any individual horse, one inherited from the sire and one from the dam.

Dominant & Recessive

If the letter that represents an allele is uppercase, it means that the allele is dominant. If the letter is lowercase, it means that the allele is recessive. Dominant alleles will overpower recessive alleles and will show even if only one copy is present, i.e. E/e will still make a horse black, even though a lowercase e is present. This means that a horse can “carry for” a recessive allele without showing it, and must be gene tested before you can be sure that they have it. Recessive alleles require two copies to show because if a more dominant allele were present, it would overpower the recessive allele, i.e. chestnut horses must be e/e.

Homozygous & Heterozygous

In other words, recessive alleles must be homozygous to show on your horse’s coat. A horse that has two of the same allele for a particular gene is homozygous (sometimes abbreviated hom) for that gene. If the two alleles are different, the horse is heterozygous (sometimes abbreviated het) for that gene. A and E are both dominant, so will show in the heterozygous state. The alleles a and e are both recessive, so will show only in the homozygous state. This is also important because some genes will express differently when they are heterozygous. This is called incomplete dominance and will be explained further down.

The Genes

Below is a complete list of genes and their alleles (beyond Extension and Agouti) that can be found on regular created horses. Not all of these genes will change the horse's color name if that coat color doesn't have a specific name, but they can still create varied and unique looks.

Pigment Modifiers

These are genes that modify the pigments of the base coats we've already mentioned. They can restrict, dilute, or darken existing pigments. Some only affect red pigment, some only affect black pigment, and some will affect both. Some genes will only show on the horse's coat when certain other genes are present. We'll get into all of this as we break it down and talk about each gene.

Agouti Promoter

agoutiPromoterGeneTestResult.jpg

When A is present on black-based horses, agouti promoter restricts the expression of black pigment even further, turning bay horses into "wild bay." It is dominant and will show even if only one copy is present. Two copies does not result in further black pigment restriction. Wild bay is still called “bay” by color name on your horse’s page.

agoutiPromoter.jpg

Dilution Genes

dilutionGenes.jpg

Cream

creamGeneTestResult.jpg

Alleles: cream, pearl, (plus two non-creatable)

Cream (Cr) and pearl (Prl) both dilute red pigment significantly and black pigment slightly. One Cr has some effect and two Cr's have more effect. This is known as incomplete dominance, which is a third level of dominance that causes two copies of the allele to have even more effect than one. Unlike purely dominant or recessive alleles, this makes all three possible genotypes — both homozygous states and the heterozygous state — have different phenotypes. The effect is so dramatic with the cream gene that these three states also each have their own color names.

As you can see, cream can be quite overwhelming when homozygous, so much so that it can be almost impossible to tell the difference between chestnut, bay, and black horses when they also carry two copies of cream. They look almost white, but actually it is just red and black pigments that are extremely diluted. (Actual white horses are covered in the White Markings section. link*) The next allele of the cream gene, pearl, is much more subtle and almost unnoticeable in the heterozygous state, but in the homozygous state, it creates a rich and metallic diluted effect.

Cream and pearl can also create different effects when mixed. Horses that are heterozygous for both cream and pearl will have slightly darker coats than the homozygous cream horses but slightly lighter than the homozygous pearl horses with also a slight metallic effect.

CreamPearlTogether.jpg

Dun

dunGeneTestResult.jpg

Alleles: dun, non-dun 1, non-dun 2, (plus one non-createable)

Dun (D) is the most dominant allele of the dun gene and dilutes the pigment of the base coat on the body, leaving the legs, mane, and tail, and often primitive leg and dorsal stripes darker (the dark areas are actually the original color). All horses with a D allele will show as dun, regardless of the base coat. Chestnuts will become red duns, bays become bay duns, and black duns have a special name — grullo. Dun is a fully dominant allele, so two D’s have no more effect than one.