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Date: Tue, 5 Nov 2002 13:13:11 -0800 (PST)
by Nicole Kinsey


Before delving into color genetics, one needs to understand rudimentary genetics. Each animal has two genes at each locus (location on the chromosome). One of each gene pair comes from each parent, so exactly half of the animal's genetics comes from each parent. Each gene pair controls "something" genetically. The vast majority of the equine chromosome is still uncharted territory. But, when it comes to colors, a lot of the answers are known. This is part of why a study of color genetics is so useful and easy for the average horse owner; and it's also an area of genetics where it's easy to visualize the results since you can SEE the horses' colors.

The major genetic terms you should understand are dominant and recessive.

In color genetics, most equine genes are simple dominant/recessive. This means they act as an "on/off" switch. If the animal has one copy of the dominant gene at a particular locus, they will express that characteristic. In order to express the recessive characteristic, the animal must have two copies of the recessive gene at that locus. Genes are often represented by letters, with the upper case letter referring to the dominant of the pair, and the lower case letter referring to the recessive. For instance, let's say we have a locus called the "X" locus.

At X, the "X" represents the dominant, and the "x" represents the recessive. Further, let's say X is a simple on/off switch; the horse either has X trait or does not. So, if the horse is "XX" or "Xx" at that locus (each letter representing a copy of the gene -- remember they have two at each locus), they have that X characteristic. If the horse is "xx" they do not have that X characteristic. Often, if a horse displays that X characteristic, you don't know if they're "XX" or "Xx" so they will be represented as "X-" as you only know that they have at least one dominant gene. Also, keep in mind that "Xx" is identical to "xX" -- it doesn't matter how it's written. A lot of people tend to get glassy stares at this point. Don't worry! It will sink in. Read on, or reread the last section -- whichever works better for you. And don't give up! Hopefully, it gets easier with real life examples.

Oh, one more set of terms (I won't use them much in this discussion): homozygous and heterozygous. Homozygous means that the animal has two copies of the same gene at a particular locus: XX or xx would both be homozygous. Heterozygous is two different genes at a locus: Xx is heterozygous. When it comes to breeding the homozygous individual only has one "option" at that locus, and will pass the same thing every time. The heterozygous individual has a 50/50 chance of passing either of it's genes at that locus.

Before getting started, I need to clear up a common misconception about equine color genetics. Many people think each horse has two color genes.

However, the horse has many many loci (plural of locus) that control color. It's not a case of "this horse has a bay gene and a chestnut gene." Just for the very basics of black, bay, chestnut, and grey, each and every horse has a black/red pair, a bay/not-bay pair, and a grey/not-grey pair. When one gets into other colors and patterns, each is an additional gene locus, not just an additional option. Don't get frustrated yet, please keep reading...

When it comes to equine color, the first thing to tackle is the "base color." Various people refer to various things when they use this term, for the sake of this discussion I'm referring to the colors of black, bay, and chestnut. Once you understand the relationship of these three colors to each other, all other colors and patterns are simple to "add on top" of the base color.

The horse's base color is determined by the interaction of two loci. This is why grasping the base color is the toughest step to understanding color genetics. After you get this relationship of these two gene pairs, you'll find color genetics is a breeze!

The first locus to look at is usually called the Extension locus. It is represented by the letter "E" (terrible letter to remember, but you'll eventually get it). This locus controls the "true" base color of black or red. Every horse, when you come down to it, is red or black. But, this is difficult to understand since bay horses are actually black-based, not red like your eye would tell you! So, let's look at Extension:

Extension is a simple dominant on/off switch. The dominant E is a black-based horse. So, horses that are EE or Ee are black-based. The recessive e is red, but only an ee horse is red based (remember that recessives must have two copies of the gene to express it). A "red" horse is a chestnut.

If you are dealing with a chestnut horse, it is guaranteed to be ee at extension. Period. All chestnut horses got a copy of recessive e or red from each parent. And all chestnut horses will pass a copy of that recessive e or red to their offspring. There are no exceptions to this.

But this is where things get more complicated and where people get lost and confused. Because this is where the bay horse comes in. The bay horse is a BLACK-based horse. So, he's EE or Ee at extension. But, this is where the interaction with the second important locus needs to be understood. This locus is called Agouti, or often the bay-modifier, and is represented by the letter "A" (agouti comes from other species, and is not totally representative of the horse, but we're stuck with it).

Agouti only acts on a black-based animal. It restricts the black to the points, creating the bay. The dominant A is the on-switch for bay. And the recessive a is the off-switch for bay. So, if you have a BLACK-based animal (EE or Ee), it will be either black or bay depending on the agouti locus. E-A- is bay. Read this as: horse with one dominant black and one dominant agouti is a bay. The actual genetic make-up of this bay horse can be one of the following: EEAA, EeAA, EEAa, or EeAa.

Alphabet soup strikes again! Sorry, folks, but for many, grasping the letters makes it much easier to grasp the overall concepts. If you're not one of those types of people, try to follow the descriptions instead.

I'll try my best. Don't shoot the messenger.

So, how do you get an actual BLACK horse? You have to have the dominant "E" at extension and two copies of the recessive "a" at agouti. That means the black horse is only one of two genetic combos: EEaa or Eeaa. This is why it's often hard to breed for black. There are twice as many genetic combos that can be bay as can be black.

So, do we understand black & bay yet? Well, it's time to muddy the waters a bit more. What about those chestnuts? They still have genes at agouti, but it does NOT express visually on their coats. Remember, agouti only acts on black pigment. So, red horses "hide" their agouti locus. But, chestnut horses will still pass one of their agouti locus genes to their offspring. That's why it's important to understand what's going on. If you breed a chestnut to a black and get a bay foal, you'll quickly want to know where the heck that came from! Chestnuts can be any of the following: eeAA, eeAa, or eeaa; so, while chestnuts can only pass "e" to their foals, they may pass "A" or "a" to them, and it'll matter if their foals get an "E" from the other parent. But, there is no way to look at a chestnut and know what they have. In fact, it can be very difficult to even look at a chestnut's pedigree and know for sure what they have at agouti. Confused yet?

Oh, and I'm sure everyone wants to know about "homozygous black," right? Well, this term refers to black horses that are EEaa. This means all their offspring will inherit an "E" and be black-BASED, but since they may get an "A" from their other parent they will not necessarily be BLACK, they may be bay. Beware of the stallion owner who says you will get a black foal -- they can't know that unless your mare is black as well, as any other color bred to a homozygous black may end up with a bay foal.

If you can grasp that extension/agouti relationship, everything else is easy!

Ready to move on to grey? Grey is really quite simple. It's a simple dominant on/off switch. A horse is grey or it's not. Grey is represented by the letter "G" (finally one that makes sense). A "GG" or "Gg" horse is grey. A "gg" horse is not grey. Grey is a masking gene. It will eventually "mask" whatever other color the horse is. But, all horses are some other color "under" that grey mask. This means this horse is black, bay, or chestnut under the grey, and will breed like a black, bay, or chestnut in addition to the grey. A "GG" horse is homozygous grey and will have 100% grey foals. Takes a lot of guess work out, well, until you get to the next generation that is. If a horse is "gg" and not grey, it makes absolutely no difference how many greys are in it's pedigree, it will never pass a grey gene to it's offspring.

Another big question is often: why did this grey x grey breeding have a non-grey foal? Simple, each heterozygous grey x heterozygous grey breeding has the odds of 75% for a grey foal and 25% for a non-grey foal.

Remember, the heterozygous grey is "Gg" so has a 50/50 chance of passing G or g. If both parents pass g then presto! the foal is not-grey.

In Arabians, this is really as far as you need to go to understand the basics of color genetics. The other main modifiers you'll see in Arabians are sabino (white markings) and rabicano (roaning through the coat). You'll also see smutty (dark hairs in the coat), and a few other minor modifiers. But, ALL Arabians are black, bay, chestnut, or grey. Everything else is additional to those four. Get the building blocks: black vs chestnut; then bay vs black; then add grey on top. And then you're ready to tackle patterns and additional modifiers!

Also, try to keep in mind that while most people will use the simplest notation to refer to colors (such as chestnut = ee or grey = G-) that EVERY horse has genes at EVERY locus. Even if the genes are all for the "off" position, as the majority of color genes are in Arabians. So a homozygous black is really EEaagg (and a lot more if one starts looking at more modifiers & patters), which is read as black/black, not-bay/not-bay, not-grey/not-grey.

So, I hope this helped at least a little. Please feel free to ask questions and I'll do my best to help.

~Nicole