An Interesting Bit on Albinism

My dad was recently talking to me about albinism because one of his insurance customers has a grown albino child. He was very interested to hear about albino, and also was fascinated when the man told him that everyone has the possibility to produce albino. This is not exactly true, but it is close.

Everyone has heard of various albino creatures, and most people know that it is a recessive gene. But does anyone actually know what that means?

Within people, there are several different kinds of albinism. The exact way of defining it is blurred by what we see in animals. According to NOAH (National Organization for Albinism and Hypopigmentation), most people with albinism do NOT have red eyes, which is often the most defining characteristic that we think of. What else is partially myth to albinism, and what actually causes it?

Albino is not a gene in itself, but what causes it is the gene that creates pigment. Similarly to any other genetics, when both genes are turned 'off', it creates no pigment. The reality of what no pigment means can actually vary widely within the individual. Some people do not even appear 'albino' by our standards. I am now hesitant to add any photos, unsure of what the truth about each individual case whether human or animal is.

The statement that 'all people carry the albino gene' is not quite true, because most people do not carry it. If everyone carried it, then one in four people would be albino. That is what makes it rare. The only time it can happen is when two people who are heterozygous (carriers of the recessive gene) have a baby, and only then there is a 25% chance of albino. 

Using the 'albino is recessive', that means that pigment genes are dominant. A heterozygote is a carrier for that recessive gene, but phenotypically they will appear like any other person. And, just because they are a carrier does not mean that every child of theirs will be albino.

Lastly, because this is a horse genetics blog, stay tune for Part Two: Albinism in Horses

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/

Re-Visiting Leopard Complex Patterns - Again

Please forgive me for any mistakes in some of my previous posts. I am still learning, and also learning that I made several assumptions on several genes that may not have been correct. Only some of the very first ones.

Using research and deduction, I am re-evaluating the guess that Chocolate carries patterning genes. My question is, which ones? 

To those of you that don't know, Chocolate is my solid black POA breeding stock mare. Both her parents were LP patterned. The genetics make sense as to why she is solid, but if I were to breed her back to a spotted horse, what spotting genes could she possibly contribute? The picture below gives you an idea of just how solid she is. Doesn't get much blacker n' that!

Because LP is still constantly being researched, some of my research may be proven not quite correct in several years. That's okay, just as long as you know it is an ongoing process.

From what I understand, LP is under current study. Actually, to be more precise, the patterning genes are under investigation; LP has been marked and is traceable through various tests. These tests are offered to the public, and don't cost much money. It is how the pattern genes work that stumps the researchers, and how they work with LP.

Here are several bullet points to remind you of how this works:


1. LP is the master switch. Turn it on, and you have varnish roan. This is easy to understand, but how varnish roan turns into leopard and blanket appaloosas is a matter of question.

2. PATN1 is the gene that the Appaloosa Project (the main scientists behind the discovery of the LP marker, and the current investigators) believes turns varnish roan into leopard pattern. 

3. Unlike what I posted before on pattern genes, PATN1 is inherited entirely seperately from LP. The marker that is what you test for in colors has not been identified. What is odd to me about being seperate from LP is that, even though they are different genes, they still work together in a drastic way.

4. The Appaloosa Project has determined that PATN1 is dominant over whatever gene causes blanket. That means that blanket horses do have have PATN1, but leopard horses could carry the blanket gene. Whether they have one or two copies of PATN1, it still 'over-rules' the blanket gene.

5. I call the gene that controls blanket the 'blanket gene' for now. The Appaloosa Project plans on calling it PATN2, yet because it has not been identified they cannot officially call it anything.

So now, which pattern genes does Chocolate carry?

The only thing I can do is make a conclusion based on pictures and descriptions. Descriptions are hard to take seriously, since so many people don't know how to differentiate patterns. However, because I am working on patterning genes and not whether the horse is heterozygous or homozygous LP, descriptions may actually mean something. It is not that hard to tell the difference in a blanket, leopard or varnish roan, and whether any of those is snowcap or fewspot is besides the point.

The trouble with patterning genes is that the outward appearance tells us almost nothing about whether they are heterozygous or homozygous for PATN1 or the blanket gene. If a horse is homozygous LP and is fewspot, that does not mean he is homozygous PATN1. Because they are inherited seperately, he could be either PATN1/n or PATN1/PATN1, but because he is fewspot it would be impossible for him to not have any PATN1. Do you follow?

Allbreedpedigree.com is a lifesaver. It really is; I would only have two generations back on Chocolate without it. Two generations is all I really need, but it also contains some photos, and the names mean everything. Here is a link to her pedigree: http://www.allbreedpedigree.com/jkb+chocolate+bar

So now, I need to look at her parents and offspring to help determine her patterning genes, or the possibility of pattern genes. She has had one blanket foal, and one leopard foal. Because both of the stallion's she was bred to were patterned, that may or may not be important.

When I do a Google search on her dam, JK Jokerette, I don't get much. I know the breeder that owns her, and he has a descriptions of his horses on this page. To quote what he says on her, "JK Jokerette “Sweetie”  ApHC 537354 mare, foaled 3/14/94 – Chestnut w/roaning and snowflakes.  14-1 hands.  This is a beautiful mare with super donformation, fantastic disposition and a Who’s Who pedigree, tracing to My Secretariat, Joker B, Bold Combatant and Bold Ruler plus her dam was half Arabian. "

I think I trust his opinion on this. When he refers to roaning and snowflake, these are terms that are used in stages of varnish roan. Because varnish is always progressive, she won't always be snowflake, or she may constantly stay with the snowflake pattern.

Either way, how I come to conclusions on this is that, because Sweetie (Jokerette) is varnish, she has no pattern genes. Therefore, Chocolate inherited no pattern genes from her. That isn't really helpful, other than I know that Chocolate can't be homozygous for either pattern genes.

Now for Chocolate's sire. JKB Bold Bar. Of all the pictures on Allbreed, they are all at least three generations back. Not really helpful. Moving on to descriptions, and other progeny.

According to the same breeder's website, he still owns the sire's dam. Here is the description: 'JKB Dilly Bar – 40640 – Foaled April, 1994; black with snowflakes."

That doesn't bode well. Another varnish roan. This means that JKB Bold Bar could not be homozygous for either pattern genes. Since he was heterozygous, this means that there is a 50/50 chance Chocolate carries pattern genes. The odds are not as strong as I expected; when I went in to this research, I thought both parents were patterned. 

If I only knew what pattern he was, it would rule out possibilities. If I knew he was blanket, then he would be recessive for PATN1 and heterozygous for the blanket gene. I would know this because PATN1 is dominant over the blanket gene. If he were leopard, he could be heterozygous for both. 

Because JKB Bold Bar's mom is varnish and doesn't carry pattern genes, lets look at his dad, Santee Super Son. From Allbreed, we know his dam was blanket. There's a picture of her attached.

When I type in Santee Super Son as a search, I don't get anything. However, there is a link to Gene Carr's website. For those of you that don't know, Gene Carr is one of the biggest POA breeders and showers in America. 

Interesting; nothing on Santee Super Son, but he has lots of stallion's with Santee in their name. I find it interesting that this particular Santee is not on his page. But wait, look at this one! On his stallion page there is a picture of Super Sun, grandfather of our Bold Bar. Great; now we have pictures of both of his grandparents. Below is Super Sun. And Here is a link to the mare he was bred to (scroll down; you're looking for R Misty Stuff)

Sadly, even though I use all my brain power, it will take more research to learn anything about these two grandparents in particular. *Sniff*. Moving on.

You know, the easy thing to do would be to just call the breeder of JKB Bold Bar and ask for pictures or a description. But this research stuff is fun!

I think the next step is to look at Bold Bar's progeny. The first one is JKB Bold Siri Delight. I can't find any pictures or descriptions on her, so moving on to the next one.

Oohh, this is interesting. Listed in JKB Bold Bar's progeny is JKB Boldbars Lucky Lady. Quite the name. Anyway, her dam is my other mare, Barbie Doll, a.k.a. Shesa Fancy Lady. Barbie carries blanket genes. So Barbie was bred to Chocolate's sire. I only have one picture of this little filly, and she appears to be blanket as well. Barbie's other son is blanket too; she might be homozygous, which doesn't give me any info on the sire. Ugh. 

Oh look, JKB Boldbars Lucky Lady had two foals as well. I could examine them to try to determine whether she was homozygous for the blanket gene. If she was, that means that JKB Bold bar carried at least one blanket gene. However, because there were only two foals, it could be just chance. Ugh.

What next? Ummmm, probably a phone call. It's a simple question.

Horse Color Genetics: Dominant White and It's Gazillion Mutations.....

Dominant white is basically a white spotting gene, similar to any of the pinto patterns. HOWEVER (and that is a big however), it is not as simple as all that.

Dominant white is not all that common, and it comes in so many different forms that it is hard to trace. There are 20 identified mutations, but only 3 you can test for. There are probably more since it almost seems like a progressive color, mutating just a little bit every time a horse is bred. That is why it is so hard to trace.

This particular spotting gene can come in all shapes and forms. The easiest to identify is almost all white; about as close to albino as you can get. HOWEVER, the eyes are dark, unlike cremello's and other double-cream horses. Think of dominant white as a huge white spot; whether it covers the whole body, or only parts, depends on the mutation. These can sometimes be mistaken with fully expressed sabino horses.

There is another way it can show up, too. It can also be more spotty, and even look sabino, or even any of the other pinto genes. On the genetics forum, sometimes people will post pictures of their unusual pinto horses that they tested for all the different genes they could test for, and still came back with recessive results. The verdict is that they must be some kind of untraceable dominant white gene. There is never any uniform pattern to partially spotted dominant white horses, unlike all the pinto patterned horses, which is also why it is hard for owners to identify.

The below horse is the founder of Dominant White 3, which is found in Arabians.

What's neat about dominant white is that it is present in quite a few all-solid breeds like Arabian and Thoroughbred, making quite a few look pinto-mix. But dominant white is accepted in those breed registries, wheras pinto is not.

It is thought, but not fact, that all of these dominant white mutations in homozygous form is embryonic lethal, resulting in what scientists think is an embryo which dies after a few weeks. This thought is based on the fact that all of the horses that have been tested for dominant white are heterozygous for the gene. Whether this is within each individual mutation or umbrella for all W genes is beyond me.

More information will be posted as soon as more information is available.  Below are all the traced mutations, but not all of the tests are available to the public yet. Check out W5!

Horse Color Genetics: Calculating Possible Outcomes

When determining possible outcomes for foals, almost everyone knows about the coat color calcuator, here. Lately, I've been practicing figuring the results without it, because I would like to know them off the top of my head.
To start, it's good to have a definite color genome because without it, the numbers are much more confusing. I'm still working on how to solve that.
Let's start with an easy one:

Ee aa + EE Aa

When starting on calculating, always work from left to right, and write it down with a pencil so you can erase the numbers to make them smaller as you get more detailed.
To solve the question, use common sense to know that the horse will always be black-based; the horse on the right is homozygous dominant for black.
So now the question: will the horse be black, or bay?
We know from the horse on the left that at least one agouti gene will be recessive. The other one is 50/50, so therefore, the outcome is 50% black, 50% bay. The possible genomes are EE aa, Ee aa, EE Aa, or Ee, Aa. The first two were for a black horse, the second two were for a bay. Even odds, making:

50% Black
50% Bay

Let's change it up:
Ee Aa + Ee Aa

Only look at the extension status to start with. The possible outcomes for just that are: EE, Ee, Ee, or ee. Why did I do Ee twice? Because you can take into account that the dominant gene could come from either one. You could change the second Ee to eE if it helps you remember which one comes from which.
Now, looking at those, 3/4 of those outcomes make a black or black-based horse. So we have:

75% black (we'll change that later once we find out about agouti)
25% red

Using the same technique as before, the possible outcomes for the agouti status would be the same: AA, Aa, aA, or aa. 3/4 makes a bay horse.
To apply this to the equation above, remember that the red status shouldn't change. That is solid; we are only applying this if the foal was black. So the real question is what is 3/4 of 75%?

Think back to math class; to figure this, multiply the 75 times 3, then divide by 4. That leaves you with 56.25; those are the final results for bay. But obviously 56.25 + 75 + 25 don't add up to 100; you now need to change the black outcome. Add up the red status plus bay, then subtract that number from 100 to get the final answer for black. That number is 18.75. Here are the final results:

56.25% Bay
25% Red
18.75% Black

Now if you add on more modifiers and dilute genes, the genetics aren't as hard as you think. Generally you just divide each number in two. For example, let's use what we have above but add in that one parent has one copy of the cream gene. Going back to the parents, their genome's now look like this:
Ee Aa Cc + Ee Aa cc (one parent is recessive for cream, and generally you wouldn't show it, but I put it in so you could see).

To calculate, first do all the above steps and you would come to the same conclusion as the above, but without the cream. Now that you've done those steps, you can add in cream. For just the cream status, the possible outcomes are: Cc, cc. Just those two. The first one has cream, the other doesn't. Because it's 50/50, all you have to do is individually cut each color in half and add in whatever that color would be with cream. Like this:

28.125% Bay
28.125% Buckskin
12.5% Red
12.5% Palomino
9.375% Black
9.375% Smoky Black

I used a calculator for those smaller numbers, but once you get a little more accustomed to doing these, there are a lot of repeating numbers such as 75, 50 25, 12.5, 37.5, you get the idea. If you compare these numbers to the online coat calculator, the only difference is that they round up on the small numbers to change 28.125 to 28.13 and 9.375 to 9.38.