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: Appaloosa Pattern Inheritance

Going back to the question that started it all, and what I determined. Can my solid black horse Chocolate with appaloosa breeding produce an appaloosa foal when bred to another solid horse?

The answer is no. Not to another solid horse, and I'll explain why.

The LP gene needs the master switch turned on. Without the master switch, none of the pattern genes work. BUT....that does not mean that Chocolate does not have pattern genes.

Both of Chocolate's parents were blanket appaloosas. But both were heterozygous for LP, and Chocolate inherited both of the recessive genes. How do pattern genes work?

You need to imagine each LP allelle seperately. Linked to each allelle are two different pattern gene options. Imagine the bunkbed, back from the KIT gene post. These mini-patterns that are linked to each main LP allelle can be either turned on or off, even if both of the main LP genes are recessive. Sort of like how a pillow and a blanket could be in the bunkbed whether someone is using them or not. I picture it like this:

LP patn/patn1     LP patn/patn1

The above shows each LP allelle seperately, with both pattern genes turned off. The first one is for leopard, the second is for blanket.

So that means that Chocolate, even though she is solid, could carry pattern genes, but the master switch is turned off. How does this translate to breeding?

Most appaloosa's carry pattern genes, so not having a pattern gene is not really a big deal. If Chocolate didn't have any pattern genes, but if I bred her to a homozygous appaloosa, then she would still probably throw a colorful foal. That is because any pattern genes the foal needed would come from the father.

This is not always the case, but I really would like to know how any genes Chocolate has could effect what LP pattern the foal could have. The stallion that I'm looking at is this guy:

He is homozygous LP, so the foal would certainly be heterozygous LP. But, within the heterozygous range, there are three pattern options: leopard, blanket, or varnish roan.

I would be so disappointed if it came out varnish roan, but because I've seen a lot of this stallion's offspring, and of the two foals Chocolate has had are super colorful, I am fairly certain that there is no chance the foal would not get no pattern genes. No pattern genes equals varnish roan, FYI.

Now, the question I am dying to know: which of the two remaining patterns is most probable?

The frustrating answer? There is no way to know. The information I want doesn't exist. Scientists are trying really hard to understand how appaloosa pattern inheritance works, but it is really hard to trace. My information that I wrote about above could be proven completely wrong in 10 years.

As a side note, one of Chocolate's foals was from this same stallion, JKB Quick Draw McGraw. The filly was a gorgeous black leopard. So I know that that is very likely to happen again. This is not the exact filly, but it did look a lot like this:

Horse Color Genetics: Leopard Complex, Part 2

Review: E=black, A=bay, G=gray, CR=cream, D=dun, TO=tobiano, F=flaxen, Z=silver, O=overo, SB1=sabino, SPL=splashed white, LP=leapord complex (appaloosa).

The first thing you need to know about the leapord complex is that it is an incomplete dominant. I know I've maybe mentioned simple and incomplete dominant before, but here is what it means. Simple dominant means that whether the horse has one or two copies of the gene, it will do the same thing. Incomplete dominant means that if you have one gene, it may look different than the horse with two.

With leopard complex horses, just by looking at them it is easy to determine whether they have one dominant LP gene or two. It is actually more simple than you might think. LP horses with spots are heterozygous (one dominant gene), LP horses with no spots (coats like few spot or snowcap) are homozygous (two dominant genes). 

One other thing that is important to know is that all horses with the LP gene are varnish roan underneath. Remember my last post? Anyway, depending on what pattern genes you get, it probably won't show that much. But if you look at the face of the horse's, you can kind of see the roaning in where there are larger patches of dark. This isn't really true of blanket appaloosa's (you can't see the roaning so much), but the presence of the white hairs to make it roan (varnish roan) will be mostly diluted.

For example:

This horse is heterozygous LP. How do I know that? She has spots! Easy. There is a 50/50 chance she will pass the spots onto her babies.

And this one:

 And this one:

They all have spots! Regardless of whether they are all over, or are only on the blanket (or both!), they only have one dominant gene. What could happen if you bred the next two horses together? (Hint: both are heterozygous, or LPlp)

Here are the resulting options:

Surprised at the last one? The different options for the first two horses to have were: LPLP (homozygous; the first horse), LPlp (heterozygous, the second one), or lplp (homozygous recessive, or not present at all).

Now on to homozygous colors. Review: homozygous means you know the horse has two dominant copies of a certain gene. 

Here are a couple horses that are homozygous:

 There is a lot of white. The first one is a snowcap, and the second one is a fewspot (literally!). These horses are homozygous. If you bred those upper two together, what do you think you are going to get? The baby won't have any spots, unless it is a few spot. 

If you remember back to my last post, the last color I mentioned was varnish roan. Varnish roan is the only LP color that is hard to tell; you may not be able to at all without sending your horse's DNA into a lab.

The last thing you may be wondering is, 'How can I tell what pattern my mare's foal will be?' Well, the tricky thing is, you can't. If it might be heterozygous, you won't be able to tell if it will be leapord or blanket. If it is homozygous, you won't be able to tell if it is few spot or snowcap (pray for a snowcap!).

One last fact that is something scientists only recently discovered. Horses that are homozygous for LP have something called CSNB. This stands for congentical stationary night blindness. A mouthful? It is exactly as it sounds: horses that are homozygous are blind in the dark. Surprised? 

You may say, "but my horse sees just fine in the dark!" I'm sure you know your horse very well, but thing is, it probably doesn't. But he doesn't know that. Can you see in the dark? Not very well. Same thing with him. If you couldn't see in the dark, and then someone told you that everyone but you sees in the dark, what would you do? You've always been that way, and there isn't anything you can do about it.

 He has always been that way, and always will be, and he won't know anything different. He has developed ways to get around pretty well in the dark on his own. There isn't anything you can do about it, and I wouldn't really say it is a bad thing to have either. I wouldn't not breed my two homozygous horses together to prevent it, even though it is inevitable to happen.

In conclusion, if you want a spotty horse, breed a  homozygous LP horse with a homozygous recessive. That way, you will have lots of color! In the Appaloosa and Pony of America registry, if you cross with certain breeds, then it is still eligible for full registry. These crosses include: Quarter horse, Arabian, Morgan, and Thoroughbred. Some spotted horse breeders keep these breeds so they can make more color and crazy spots. 

Horse Color Genetics: Leopard Complex, Part 1

Review: E=black, A=bay, G=gray, CR=cream, D=dun, TO=tobiano, O=overo, F=flaxen, Z=silver, SPL=splashed white, SB1=sabino.

In this first post, I'm going to show you the different coat colors, and then get into the genetics and how they work in the second part of the leopard complex.

The genetics to the appaloosa complex are very tricky to understand, and I'm still trying really really hard to understand more about how the pattern genes (modifiers to the appaloosa gene) work.

The correct term for appaloosa complex is leopard complex. LP. This gene is seen in the breeds like the Appaloosa, Pony of America, Knabstrupper, Colorado Ranger, and Miniature horses. When I refer to appaloosa in this post, I mean spotted horses, not necessarily the breed. The breed is capitalized.

When a horse inherits the LP gene, the first thing you need to understand is the characteristics that they receive. Regardless of the pattern genes, whether they got one or two dominant LP genes, the traits they will always have are:

Mottled skin (sorry for the gross picture!)

The sclera of the eye shows (the white part)

And lastly, vertically striped hooves.

A horse will have these three things whether they have one or two dominant LP genes. Some horses with LP may or may not have mottled skin on their muzzle, but their private parts will be spotty.

So, as in other color modifiers, there is always a base coat. To make things easy, I'll use chestnut, ee,aa. Remember, no matter what markings or color, they will all have the LP traits. Starting on down the list, I'll begin with the colors, beginning with the easiest to identify. 

The horses below are leopard appaloosa. Leopard appaloosa's have spots all over them, and the name is easy to remember. The size of the spots doesn't matter (well, a little), nor the color. Out of these three horses, which one is not an appaloosa?

If you guessed the third one, you were correct! This guy is flea-bitten gray. Here is the different post on that; gray horses don't have any LP traits.

The first horse's base coat is bay (see the little black wisps in her mane?), and the second horse's base coat is black. 

The next color is a blanket appaloosa. Blanket appaloosa have white bums; the white can be only a tiny little section, or it can nearly cover the entire horse! Technically, on the white there can be spots or no spots, but for the sake of genetics I am going to say that blanket appaloosa's always have spots. Aren't they pretty? The first is a bay blanket, the second is a buckskin blanket.

The next color is snowcap blanket. Snowcap blankets have a blanket, but without spots. It should be pure white. Genetically, snowcap and blanket are different.

The next color is few spot. Few spots are a bit uninteresting to look at, but they are important to the LP gene. Few spots may look a bit like cremello, but have LP traits. They can literally have enough spots to count on one hand, or a little more than that. Some can have roaning associated with the LP gene in their 'corners'.

Another color associated with the LP gene is called varnish roan. Varnish roan is different than normal roaning. You may or may not be able to see the difference from the first two horses and the last horse, but varnish roans carry the LP gene and have those traits.

Those are the basics. There are others that you may read about, but they are pretty rare. These are the most common and make the most sense to explain.