Albinism in Horses

To follow up with the promised post after the last one, I of course have to talk about albinism in horses. To recap, albino is when there is no pigment in the skin; all genes that control color are off.

There are quite a few curiosities on the subject, including a simple fact that will surprise you: albinism has never ever been proven in horses.

While you may be able to Google quite a few images of horses that appear albino, there has never been a case in which they weren't able to prove it was something else. The horses above came up in the search, as well as the ones below.

As mentioned in the last post, red eyes only sometimes indicate albino, and there are several other things besides that would. However, with horses, there is no picture I can find of a horse with red eyes that doesn't look photo shopped, or when you look close up are actually blue eyes surrounded by pink skin.

According to various sources, blue eyes in horses is not exactly lack of pigment, and is as close to non-pigmented eyes as you can get, but again there isn't no pigment.

The most commonly mistaken color for albino is cremello, because of the very light-colored skin that often is pink with blue eyes. However, using the method of deciphering albino as in the last post, albino has no base color, and there is no pigment behind it. Cremello is a chestnut horse with two cream genes, so it would indeed have some pigment. Other double-cream horses (perlino, smoky cream) may be categorized among cremello in being mistaken for albino.
If you were to take the tiniest bit of red paint, and then add a dose of white, it makes pink. If you add even more white, it becomes light pink. Even if you keep adding white to the original red, the paint will never be truly white, no matter how much you put in.

One of the closest things to albino scientifically is dominant white. Dominant white is considered to be a white-spotting genes, along with patterns such as tobiano and frame overo. The main difference with dominant white is that it often shows up as one, huge spot, entirely covering the body and blotting out the under color. Did you notice that last sentence? 'The under color'. There is a color under there that they can pass on.

Dominant white can be expressed in many different ways, even within each specific mutation. It isn't always predictable, and because of that it isn't a fool-proof way to describe as albino. It seems like most of the time, it leaves the eyes their original brown color, although there are some cases of white. That would depend on the specific mutation.

Fully-expressed sabino is similar to dominant white, except that sabino never causes blue eyes, leaving the eyes dark.

So, I guess the underlying question is: why? Why has albino never been proven in horses? Why would horses be the exception?

Albino means there is no pigment whatsoever, and they never have any color to pass on. With all these genes, the horse also has a color underneath. The only way for a horse to be albino would be that somehow, the gene that causes pigment (extension) wouldn't be working.

Extension is the only gene that causes pigment. All the rest of the genes I speak of are simply instructions, or a way to lighten what was already there. Isn't that interesting?

For albino to happen, extension would have to find a way to not work. Because it is a dominant gene, one or two copies produces black pigment. In recessive form, it causes red pigment. That doesn't leave any option open for no pigment, see?

In the whole history of horses, we haven't found a way for it not work as of yet. Albino hasn't happened yet, that doesn't mean it can't. Extension would have to find a way to be missing entirely from the genome, but how when both parents have it boggles my mind. Colors, and the way they work, and the way we percieve them is constantly changing.

What Does Phenotype Mean?

On the Equine Genetics page on Facebook, there are a lot of people that use the term 'phenotype'. What does it mean?

It is a word that means 'the physical appearance of something', although a lot of people that use it have a way of, even on the internet, sounding snobby because a lot of people don't know what that means. And that is ok! I don't use it because it is just one more long word that confuses people.

In an example of how to use it: a black horse with one cream gene is called smoky black, although phenotypically, it may look the same as a normal black horse. Can you tell the difference in the horses below? Probably not. Phenotypically (or, the way they appear) they are the same.

Or: a chestnut that carries dominant agouti will have the same phenotype as one without.

See what I'm saying? Now that you know the word, you may want to be careful who you use it around.

Here is a post I did on several differences between horses who have the same genes, but different phenotypes: http://michaelashopeandhorses.blogspot.com/2014/11/horse-color-genetics-differentiating.html

What Exactly is the Job of Extension and Agouti?

Since my previous post on basic genetics, the one in which I talk about base colors, I explained that dominant extension makes a horse black, and recessive makes red, and if a horse carries dominant black and dominant agouti, it makes bay. In a sense, basically what I am saying is that a horse is either black based or red based, but that isn't true.

If you assume that what I said about the dominant form of extension makes black and added on top of that makes bay, then I am basically saying that agouti is a modifier. Agouti modifies extension. Read that statement again:  you will see the fault in it. If agouti is dominant, and is a modifier, then it would modify all extension, yet science dictates that that agouti only modifies dominant extension. In that case, it wouldn't be dominant. Somewhere, there is a breakdown that doesn't make sense.

Basically, erase everything I ever said about agouti being a modifier, and pay close attention: the order in which we mentally play out colors doesn't actually work the easy way. 

The truth is that extension does not create black pigment; extension is present in horses that are not black. That being said, what extension does is it creates black and red pigment. The dominant form of extension creates black, but when paired with agouti what exactly happens is a bit mixed in people's minds.

Think of agouti as instructions: it instructs the black pigment where to go. Even in recessive form, they are still instructions. Agouti is still telling the black where to go. 

So: DO NOT THINK OF EXTENSION AS THE BLACK GENE, AND DO NOT THINK OF AGOUTI AS THE BAY GENE. Because in truth, agouti makes both bay and black. Does that make sense? The absense (or recessive form) of agouti is actually what makes the horse solid black, and even if the horse was dominant for extension and agouti didn't exist, then maybe the horse wouldn't be black at all. 

Agouti does not add or dilute red pigment to make a black horse. This is not particularly important in actually understanding how colors work, and if you read this to a beginner it may make no sense whatsoever. The basic 'extension makes black, and agouti makes bay' will work up to a point, but understanding that agouti does not modify 'what is already there' is nice to know at some point. And it is science, and trying to make it simpler than what it is is fine, but NOT simplifying it into something not true.

For further reading, go to http://equinetapestry.com/2014/09/bay-is-not-a-modifier/

Horse Color Genetics: Re-Explaining Heredity and Basics

To go back to the basics, as I've learned more about genetics I have thought of better ways to explain how it all works. My first post about heredity was fine, but I thought I would re-write it with a different example.

Let's start with a genome sequence: Ee, AA, Cc, LPlp

If you've tried to understand genetics, then you may have seen something like this. This is a way to abbreviate the horse's color, but being able to read it is what takes practice.

For each individual gene, there are two alelles together that make up the gene. Each alelle individually has the chance to be either 'turned on' or 'turned off'. The 'on' genes are capitolized. The 'on' genes are called dominant, and 'off' genes are recessive. If I ever refer to dominant and recessive, always think of a light switch. If they are reccesive, the light switch is turned off.

When any creatures breed, each parent must give only one alelle from each gene to it's offspring. That means when they breed, the gene will split, and the depending on the parent, they will get either two on genes, one of each, or two off genes.

Using the example above, the gene AA was both turned on. When both genes are turned on, or both turned off, this is called homozygous. 'Homo' means the same; both allelles are the same, and you know what the baby will inherit.

The rest of the genes, Ee, Cc, LPlp, are one of each. That is called heterozygous, 'hetero' meaning different. If this horse were to breed, we can only make a not very good guess as to what color the baby will be, because it is 50/50 whether they get the 'on' gene or the 'off' gene.

If you are still confused, let's use flowers for a simple example. If you breed a red flower and blue flower together, the baby will be purple. One red gene from the red flower and one blue gene from the blue flower. However, the genes inside the baby will still be red and blue. If that baby were to breed with a red flower, then those genes would split. THAT baby would get one red gene from the red parent, and either a red gene OR a blue gene from the purple flower. So that baby would either be red or purple.

So if I were to say that the horse in the example is heterozygous E, that means that there is one dominant gene and one recessive gene. If I said that the horse was homozygous dominant A, that means that both A genes are turned on. It is important to know that when I refer to homozygous, I usually mean homozygous dominant, meaning both genes turned on, versus homozygous recessive, both genes turned off. When a breeder advertizes their stallion for a certain homozygous gene, they are referring to homozygous dominant.

I'll use a different post to go back and re-teach you about the basic colors, and how all this applies.

Horse Color Genetics: Differentiating Shade and Actual Color Difference

On a genetics forum on Facebook, a lot of people often times get mixed up with the 'shade' of the color, and would like to call it something else, when genetically it is the same. But a lot of stumping happens when one horse is so dark or light it is easy to think they are a different color than they actually are.

For instance, one person posted a picture of a horse that was so dark red that it looked black. In fact, at first glance I thought the horse was black. Upon second glance, I had no idea. It looked a lot like the horse below.

Here are some options this horse could be; faded black, smoky black, or dark red. My vote is red on the horse above. That's pretty weird, right?

Same for the horse's below. They could almost be palomino, but they are actually red.

So now, I guess the question is, when does it matter? How do you know when it is one thing, but it looks another? Why do genetics matter if the horse doesn't actually look like what it's genetics are? 

To say the truth, most horses look like what their genetics are. There will always be slight exceptions, especially in the coat pattern tobiano. 

For tobiano, there are certain characteristics that they normally would have. They main one is white crossing over the back, but strangely, in minimal tobiano, it is the rule that is broken the most. Like the horse below looks tobiano to me, but the white does not cross over his back.

Back to the main question of shades; when do shades matter, and when should they be ignored?

To me, shades don't generally matter, unless they cause you to question the 'genetical' color. Like the first horse, who some might call black, but is actually red. There are certain colors in which the shade does matter. Like bay dun or dunskin (buckskin plus dun), the difference being that one carries the creme gene, the other does not. Their offspring could be totally different, but the only way to tell without testing is by the shade of tan.

Genetically, these two horses are different. Kind of weird, huh? The first one is bay dun (some might call it just dun), the second is dunskin. How do I know? The first one is more tan, the second is much more gold. The creme gene sort of enhances the dun color and makes it a lot more bright or metallic. The difference in offspring is that the first one can pass on dun, while the second could pass on creme, dun, or both.

One case that constantly gets on my nerves is when people ask whether their horse is sorrel or chestnut or red. That is one case in which it doesn't matter, unless it is extreme, like the first horse. Or another one: what shade of bay is my bay? Cherry, mahogany, or blood bay? Honestly, that is one of the most insignificant questions ever, when they almost look the same. The only time that one would matter was if the horse was dark bay, or seal bay or brown. Even then, there is only a slight genetic difference.

All that to say, there will always be a couple horses who break the rules, especially with paint, and some horses that continue to stump people. I have heard of paints who the owners tested for every single paint coat pattern there is, and each one came back negative. In those cases, they are unknown mutations of paint no one knows how to test for.

Horse Color Genetics: Wild Type Bay

Skipping the genome sequence review....

What is this wild type bay that you speak of?

Well, a wild type bay horse is a bay that has the black restricted to the mane and tail, and only a little on the legs. It's abbreviated by A+.

A+ is a different kind of agouti gene, but it still is agouti. Because A+ is dominant, even if the other copy of agouti is just a normal old A the horse will still show up as A+. Wild type bays are fairly uncommon; I've never personally seen one.

Wild type bays are typically a lighter color. Don't get me wrong, that doesn't mean that all lighter colored bays are wild type! There is a difference. Here's a good question: Is the horse below a wild type bay?

The correct answer would be no, probably not. While the legs may be covered up with white, you can still see that his hocks are black.  Besides, he is a very average shade of bay, and not particularly light.

Horse Color Genetics: Seal Bay

Okay, I'm not going to do a review of all the letter sequences again, I'm guessing you will know what I mean if I refer to them.

One question that seems to come up a lot on a certain Facebook page for Equine genetics is, 'What is brown? Does it actually exist? And how do I define it as a color? How does it work genetically?'

First, let's talk about what brown actually is. When you think of brown, you may think of the color dubbed 'liver chestnut'.

This horse is pretty brown, right? There almost isn't another word for it. However, 'liver chestnuts' are genetically the same as a normal chestnut.

Kind of weird, I know, but true. So, back to the brown question. Does it actually exist? In a sense, yes. Well, the correct term for it is seal brown. What causes brown, and what does it look like?

While you may be confused, because this horse certainly doesn't look brown, that is only the name for it. It is also called seal bay, which is more correct.

Genetically, a seal bay (that is what I prefer to call them) horse has almost the same genome sequence as a normal bay. How do they look so different?

There is actually a different case between these than the first two chestnut horses. While they were very similar in genetic makeup and it was only due to how much black was incorporated in their coat, the bay's are different.

The difference is that the seal bay horse is the result of a different kind of agouti locus, abbreviated by At (actually, the t is supposed to be smaller). It isn't exactly a mutation, because many horse's have it, it is just a different kind of agouti gene. To non-genetic junkies such as myself, it is usually called dark bay.

One very confusing thing about seal bays is that they easily confused with black horses. Here are a couple pictures of both mixed together so you can see the confusion.

Just to help you lost folk out there, the first and third one's are black. They are, what you might call, 'fading black'. My own horse is a fading black, most black horse's are. Some happen to fade more than others. But can you see the difference? Most seal bays are lighter in areas such as the muzzle and flank area, while real black horse's tend to fade all along the belly and the muzzle will stay dark.

Just to put a smile on your face, here is a super cool Shire that is seal bay.

Horse Color Genetics: Base Coat Colors

All horse colors are derived from red (chestnut/sorrel). Surprised? It is really that simple. All horses either have dominant or recessive of these two colors. The status of what color they are and which are domiannt or recessive is shown with what I call a color genome sequence. The length of this sequence can be long or short, depending on how simple the color is.
In a horse that is red, all the color genes in it are recessive. Red is really the base to all coat colors, even black. Red is not really a color gene, every single horse has it. To define red, any redish or brown horse with the same color mane, or slightly darker or lighter. Red is the same as chestnut and sorrel in the genetics world.
If you can pretend that for a minute that horses are buckets of paint, please do. A red horse is like a white bucket of paint. A black gene can come in and completely change the color, diluting the color until it is gray.
Keeping in mind that red is the base for every color, how does a black horse get black? If every horse is red, a black horse inherited a dominant black gene. This made it black. It doesn't matter whether it got two dominant black genes or one, it will still be black.
Here is a red horse; a red horse has recessive genes for every other color except maybe for bay (I'll get to that in a minute).

Because every horse is really a form of red, there is not code for red; every horse has a small code for what it's genetic color is (what it can pass on, whether each color is homozygous or heterozygous, etc.). Some more complicated color patterns are a little longer, but no matter the color, the amount of black is always shown.
Black is represented with an E. Capitol E is dominant, lowercase e is recessive. If a horse's color code is ee, then it is not black. Simple. The chestnut horse above is ee, I can tell by looking at it. If a horse is Ee or EE, then it will be black. The horse below looks like a Fresian, so it is probably EE. All Fresians are black, which you can conclude that all Fresians are dominant homozygous (so you know that two black horses make a black).

If the black horse above had not received any dominant genes (you could think of dominant and recessive like positive or negative), then it would be chestnut.

Now for a more complicated color! Is your brain hurting yet?
Bay is another base coat. It is a red horse with a black mane and tail, and black points. When I say points, it basically means the outermost edges (mane, tail, legs, the tips of the ears).

So genetically, how does this work out?

This is another gene. Remember, every horse is red until you do something to it. The bay is a red horse who has inherited either one or two black genes (it doesn't matter whether there is one or two). But it can't only be black genes, because then it would be black! A bay horse also inherits one or two bay genes (again, it doesn't matter). This pushes the black to the outermost edges.

Here is where it gets even more confusing. Some red horses carry one or two bay genes inside them and you wouldn't know, but if there is no black to push out then it won't be apparent from the outside. The representation for the bay gene is A. AA homozygous dominant, Aa heterozygous, and aa for homozygous recessive. 

Black is a dominant gene; this means that if they have only one dominant E gene, it will take effect. However, bay is not, because it is incomplete by itself. 

*As a side note, usually when horse breeders refer to their homozygous stallion, they are advertising the dominant gene, not the recessive. They do that because people like to know what they are getting :).