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Revised: Sheila Archer copyright 30/10/2002. No portion of this document may be reproduced without permission of the author. OUR special thanks to Sheila for her generous permission of allowing us to put this article on our website!

I am an independent researcher studying the genetics of Appaloosa colour patterns. My interest in the puzzle of what makes Appaloosas look like they do dates back to my first riding lessons. The stable I learned to ride was home to a chestnut leopard Appaloosa stallion named "Thunder". Every spring his foals arrived, each different from each other, and most puzzling of all, not one looking like "Thunder". My desire to understand what I saw has never left me.

In the pages which follow I will define key terms, discuss previous research by others on this topic, and share some of my own recent findings. Though my research is far from complete, this article is an attempt to bring clarity to some fundamental areas of concern in the Appaloosa breeding world. I am providing this genetic information in the hopes that it will be used for the enhancement and continuation of the Appaloosa and its distinctive coat patterns.

The main gene responsible for white Appaloosa colour patterning is known to geneticists as the "leopard gene", or Lp. This is the essential gene that a horse must inherit in order to exhibit the white patterning we recognize as belonging to the Appaloosa. In Diagram 1, the familiar range of spotted white patterning can be seen. It’s important to realize that the amount of white patterning is on a continuum. Though many labels exist to describe variations in the appearance of Appaloosas, there is no such thing as a "blanket gene". A horse carrying the Lp gene may show only minimal indications of its presence, such as white sclera and mottled skin, but if other white pattern helping-genes are also present, the horse may have quite a bit more white on its body, perhaps so much we call it a leopard. No matter what the amount of white patterning, all the spotted horses in Diagram 1 have one Lp gene. The level of white patterning is controlled by other modifying genes, some that enhance it, and others that damp it down. It is these genes which are the focus of my research.

(Click on diagrams to make larger)

Thanks to the work of Sponenberg, Carr, Simak and Schwink (1990), we know that it’s reasonable to consider the fewspot – snowcap continuum in Diagram 2 to indicate the presence of two white pattern Appaloosa genes. A homozygous Appaloosa (LpLp) will produce offspring with Appaloosa colouring and/or characteristics 100% of the time, regardless of the breed it is crossed to (Diagram 3), because it gives one of its two Lp genes to every offspring. Note also from Diagram 2 that homozygosity in Appaloosas with less than 20% white patterning levels may be very difficult to verify visually. While there may be other physical signs that indicate homozygosity, these have not yet been confirmed in published studies.

The findings of Sponenberg, et al, concerning the nature of the white Appaloosa gene are useful to both breeders and researchers. We now know that Lp is a dominant gene of some type. The way in which Lp behaves in homozygous Appaloosas appears to show incomplete dominance – meaning two Lp genes have an additive effect in the blocking of pigment to the skin and hair. A single gene blocks some pigment, but spots can still form through white areas. The presence of two Lp genes stops almost all pigment from forming either in skin or hair in the affected area, and very few spots "reach the surface" through the pigment-blocking effect of a doubled Lp, thus the name "fewspot".

This additive effect is identical in nature to that of the Crème dilution gene (Cr) as observed in palominos and cremellos. If you cross two palominos, half your resulting foals will be palominos (Crcr), while you will have a 25% chance of either getting a cremello (CrCr) or chestnut (crcr). The crossing of two spotted (heterozygous) Appaloosas works exactly the same way. As you can see in Diagram 4, crossing two spotted Appaloosas will produce a spotted Appaloosa (50% chance), a homozygous Appaloosa (25%), or a solid non-Lp-carrying horse (25%), one that has not inherited the main gene for white Appaloosa patterning. This horse will have no coat pattern, white sclera or mottled skin, nor will they appear later in the horse’s life.

Until there is a lab test for Lp, the current method of physical inspection of solid Appaloosas is all we have. When it has been decided that the horse is definitely non-characteristic, it should be recognized that this is still potentially a useful breeding animal. This horse many have inherited at least some of the white-helping genes that assist the white Appaloosa pattern gene (Lp). It can potentially transmit these to its offspring, and help to produce a coloured Appaloosa in this manner, as long as it is crossed to an Appaloosa that can guarantee an Lp gene to its babies… and your best odds are crossing to a white one!

This is a critical question, and one worth studying in detail. Let’s begin by remembering that the white Appaloosa pattern gene has a host of modifiers, genes that interact with the action of Lp. Appaloosas inherit many other genes from their parents besides Lp, some of which directly affect how much white patterning appears in the coat. Think of Lp as a light bulb on a dimmer switch, and the modifiers as agents that either turn the dimmer up or down.

In crossbreeding situations, where a homozygous Appaloosa is bred to a non-Appaloosa, each foal will inherit a different number of modifying genes that help or hinder the expression of white patterning. Most will inherit about 50% of what their Appaloosa and non-Appaloosa parents carry for pattern-affecting modifiers. It is this variation of the number and type of modifiers inherited which produces the range of white pattern levels in the offspring. As you will read further on, there are major effects created by some of the white modifiers that further complicate this picture.

So why do colour levels in some breeding programs remain higher than in others? One reason is very simple. Appaloosa breeders who cross leopard to leopard maintain a high number of the colour-helping Lp gene modifiers in their breeding stock. Each offspring inherits lots of white pattern enhancers, since both parents have a relatively "full deck" themselves. Of course, one out of every four leopard to leopard crosses will not inherit Lp, but they still carry all those colour-helping genes, and are therefore potentially valuable for breeding stock.

On the other hand, many Appaloosa breeders choose to crossbreed to non-Appaloosas. Diagram 5 shows what happens when a spotted Appaloosa is crossed to a non-Appaloosa. Now the odds of producing a foal with the Lp gene are only 50%. Every time a crossbreeding is done, the resulting foal, even if it does inherit the Lp gene, stands to get only the colour enhancing genes its Appaloosa parent was carrying. Since genetic material is a 50/50 split, half from one parent and half from the other, on average, the foal gets only 50% of the helping modifiers its Appaloosa parent had. Now you can see why the "dilution" associated with crossbreeding occurs. You can’t dilute a gene – a horse either inherits Lp or it doesn’t. However, you can gradually reduce the number of white-helping modifiers, even with the passing on of the main Appaloosa gene. It won’t be many generations before the white patterning is gone, and you are left with a horse with a solid coat, white sclera and mottled skin, the only evidence that Lp is there.

This drop in white pattern levels through crossbreeding was verified in the data I collected from the offspring of a chestnut fewspot stallion named Silver Chinook (ApHCC 27862). This stallion’s white pattern level was 95%. When crossed to non-Appaloosa mares, he produced chestnut-based foals ranging from leopard to minimal flecks, with the average being 55%, just over half of the stallion’s own white level. Interestingly, instead of these foals appearing on a bell curve with 55% as the centre, they are grouped into two clusters, one with high white levels similar to the stallion and the other extremely low. This bimodal distribution appears in several other stallions in the E-effect study, and has led to the development of a new study that further investigates the inheritance of white modifiers.

Here’s where the results of my current research come in to play. In one on-going study I am working with a large-scale Appaloosa breeder who produces over 150 foals a year. Over the past three years I have kept track of the relationship between the base colour of the foals and the level of white patterning they displayed. On average, controlling for colour levels of the sire and dam, chestnut foals tended to have higher colour levels than the bays and blacks, by a difference of about 40%.

These findings are supported by the results of a study by Woolf (1990) of white face and leg markings in Arabians. Woolf showed that chestnut (ee) horses have the highest levels of manifestation of these white markings, while bay or black (Ee) show lower levels, and EE horses the lowest of all. Believing I was observing the same phenomenon with white Appaloosa patterning, I began a study that isolates this effect.

The E-effect study which I am now in the process of completing is a phenotype analysis of the foals of homozygous Appaloosa stallions produced by low, no-colour and non-Appaloosa mares. These mares are assumed to contribute little to no white-helping modifiers to the foals, with the stallion being the major source of white patterning genes. In addition, each stallion must not be homozygous for E. Each must have two sets of foals, those which carry E (bay/black/darkpoint dun), and those which do not (ee-base coats, including chestnut/palomino/red dun). With all other variables being controlled, any difference between these two foal groups in terms of levels of white patterning are assumed to have been a direct result of the presence or absence of E.

I now have complete data sets from eight stallions, with more in various stages of completion. The ten which have the largest number of foals combined with relatively equal numbers of E and ee-carrying foals will be selected for inclusion in the final published study. To date, all the data sets reveal an "E-effect", suppressing the apparent white pattern level on the E-base coat foals by an average of 15%.

Taken individually, the data sets show an E-effect ranging from a few percent to 40%. The clearest and most extreme example of the interaction of E with Lp comes from my analysis of the offspring of the bay fewspot stallion "High Sign Nugget" (ApHC #474761) who has a near-100% white level. Since this stallion’s white levels are so high, many of the mares that have been bred to him are low or no-colour Appaloosas. As well, because of his performance as a championship reining horse and the fact that he is homozygous for Lp, many non-Appaloosa mares have been bred to him, so his total number of foals is very high, and makes for an excellent statistical picture.

"Mighty Deck Charge" Bay blanketed colt 50% white

Black (E)-based Foals Average White Level = 40% white

 

As you can see from these two data tables, High Sign Nugget has consistently produced chestnut leopards, while most of his bay and black offspring are blanketed. It is clear in this data set that, when present, the black gene (E) is suppressing white patterning. The minimally patterned E-base foals were not tested for homozygosity for E, but it is likely that this is the case, paralleling the findings of Woolf’s Arabian study mentioned above.

The best way to understand this is through an example. Take two fewspot stallions, one a bay, and the other a chestnut, both with 90% white levels. Breed them to identical twin (I know there’s no such thing!) non-Appaloosa mares. If both foals produced have the same base colour, the foal from the bay fewspot sire will have a significantly higher white pattern level than the foal sired by the chestnut fewspot. The reason is simple – in order for it to have the same apparent level of white as the chestnut stallion, the bay horse has to have more or stronger white-helping modifiers. You may have to do this experiment a number of times to get the difference to show in terms of averages of the two stallion data sets, but it will be there.

What this implies for Appaloosa breeding is significant. Eumelanin, the black/brown pigment present in highest amounts in E-base coat horses, "outshouts" white pattern genes more than eumelanin, the red/gold pigment. This suppressing effect by the black gene (E) gives a clue to the long-unsolved mystery of AQHA "outcrops" that had dams that were dark-base coloured "roans". Those mares were carrying hidden colour power which their E-base coats did not reveal. Cross the right horses together, or go from homozygous E dam to heterozygous E offspring, and presto – blanketed foal.

Since many breeders strive to produce E-base coat foals, particularly black, the E-effect must be taken into account. For example, let’s say you have a chestnut snowcap stallion with a 30% blanket, and you want to produce black foals with blankets by crossing to non-Appaloosa black mares. Even under ideal transmission circumstances, the E-effect in his black foals is going to suppress his white pattern "package" by at least 15%. His foals may only have 15% white pattern levels at best, and that is provided they inherit all the white-helping modifiers he has. Lacy blankets and minimals with white flecks are the probable outcome of this program.

On the other hand, the easiest base colours to "put white on" are ee – chestnut, sorrel, liver, red-point dun or palomino. They tend to show high levels of white patterning easily, because red pigment interferes less than black with the appearance of white patterning. Note that these are the horses that also tend to roan the most, as well as have the highest stockings and the biggest blazes. It is quite likely that all white pattern genes respond to E the same way, though this remains to be proven.

Taking the E-effect further, it can be seen that the presence or absence of E influences other pattern features of Appaloosas. In particular, ee-base Appaloosas tend to have relatively smaller and more widely dispersed spots than do those with E-base coats. Heterozygous (Lplp) chestnut-base leopards and blanketed horses sometimes have a mainly white rump, with more spots forward on the body and down the legs. It stands to reason that the pigment has a bigger battle in the rump area where the genetic command to be white is most concentrated. For this reason, breeders are advised to reserve judgment on a chestnut horse claimed to be a snowcap. Homozygosity in low white pattern level ee-base coat horses cannot be confirmed by visual inspection – only a production record will reveal the truth.

Like other complex traits, Appaloosa colouring is probably controlled by a combination of additive and non-additive genes. This makes for some extreme variations in possible breeding outcomes. Additive genes increase white patterning when a horse inherits the same one from both parents. This means a foal inheriting the same additive gene from both parents will have greater white patterning than either parent shows. On the other hand, I have collected strong evidence that at least one major white modifier is non-additive. If an Appaloosa inherits it from both parents, it will appear to have less white patterning than either parent shows. This is because non-additive genes "turn off" when in a homozygous state.

The action of the various white-helping modifiers in Appaloosas is the subject of a new study currently in the planning process, involving both a photographic survey and DNA analysis. Dr. Philip Sponenberg and Dr. Rebecca Terry have joined with me in this search, which will begin early in 2003.

While I am definitely not advocating breeding for colour, I am concerned for the Appaloosa’s future. Evidence clearly points to a lack of colour strength in the modern Appaloosa gene pool. At the current rate of crossbreeding, particularly to AQHA horses, the majority of which are chestnut, it is only a matter of time before the level of white patterning in the registered Appaloosa gene pool becomes critically low. Already, many major Appaloosa sires are chestnuts with less than 50% white patterning.

Based on my findings to date, it appears that to avoid losing the colour potency of the breed, a conscious effort will have to be made on the part of breeders to collect and concentrate white-helping modifiers in their herds in order to counteract the effects of crossbreeding. It is the high white pattern level bay and black Appaloosas that you must look to for colour strength, and to the white homozygous Appaloosas for continuity, in order to breed generation after generation of colourful Appaloosas.

• Minimize crossbreeding, or consider "closing the books"
• If crossbreeding, use bay or black, highly-coloured homozygous Appaloosas
• Do not crossbreed two generations in a row
• Select horses with the highest available colour levels when considering chestnut-based Appaloosas for breeding animals

Use non-characteristic Appaloosas from high white-level breeding programs over those from low ones

N/H horses DO exhibit the disease and DO pass it on to their
offspring 50% of the time. H/H horses are more severely affected
and more likely to die from the disease. These animals pass on
the disease 100% of the time if bred. Basically an excessive amount of
circulating potassium in the blood causes muscle paralysis and
spasms in affected horse.

These horses have a genetic fault in the sodium channels of the
nerve cells. Nerve cells transmit messages (or fire) when sodium
flows through portals in the walls of the cells, setting up an
electrical current thorough the cell. (Sodium is an ion, or a
charged atom). Potassium is also involved in the function of the
nerve cells. The excess potassium in the blood disrupts this
process, causing prolonged erratic firing of the nerves.
Affected horses always have minute muscular spasms within their
body. This causes the muscles to constantly contract and release
and this produces more muscle bulk in the affected animals.

When an infected horse is stressed, fed to much potassium, etc
the animal may freeze in place temporarily during a minor
attack, and may also experience tremors in the muscles. In more
major attacks, the horse will collapse and fall to the ground in
flaccid paralysis. They may also experience shuddering muscle
spasms. This is NOT a seizure, the horse is fully conscious
throughout the attack. If the attack is serious enough, the
horse may die due to paralysis of the respiratory muscles, thus
causing heart failure.

How do I halter train my horse?- submitted by Kim Clark, Fla.

First, regardless of age (except anything younger than weaning age), I use a long lead with a chain. You need a long one because you occasionally get a horse who has more "fight" in them, and you need to be able to get back away from them--out of striking range of the front feet. I take them to a clear area--pasture without trees or arenas work great--although I have done it in a crowded show pen in the warm up area several times when I had to show someone else's young horse that could barely lead, much less knew how to stand still. Don't worry with trying to set any feet at this point--it's just a waste of time. Get in "the leading position" (beside the horse, up near the throatlatch) and cluck to the horse and lead it for a few steps. Then stop and step out in front of the horse. The goal here is to teach the horse not to move forward unless specifically asked to (getting in the leading position and clucking). When you first step out in front of the horse, more than likely it will try to follow you to some extent. As you are facing the horse (don't be too close), pull toward you on the lead (with the chain) and say WHOA fairly deeply and somewhat stretch the word out. More than likely, you will get little to no response (as far as a whoa) the first time, as they will want to try to come toward you because of the pressure of the chain under their chin. Again, you pull on the lead (firmly and pretty steady on the pressure--not so much of a
snappy "jerk") and say whoa loudly. Again, they will probably try to step forward. You keep repeating this action, even increasing the amount of pressure you put on them if you need to, until they do whoa.  BEWARE, some horses--especially young horses who aren't used to a chain, very well may rear and strike out at the lead (thus the long lead) so you need to be in an enclosed area (if in the pasture, have the gate closed) just in case they were to get away from you--try not to let that happen. I haven't seen many older horses (yearlings on up who have had chains used on them before) really do much rearing and pawing, but it occasionally does happen, so just watch yourself. When you get your first noticeable bit of "whoa" from them, walk up and loosen the chain (their reward) and pat them and talk to them. If they move, (most of them will thinking they're finished) repeat the process. I know it sounds like it takes a while, but really most horses pick this up in 5 minutes or less. You ask for them not to come forward--that's it. In the end, you should be able to put your body weight on the end of the lead without them taking a step forward. Now I don't mean put your whole body weight on a weanling or early yearling, but a significant amount of pressure (nobody have a fit--this is just how it works) and I am smaller than some--especially men (I'm 5'4" and about 120 pounds).

Once they are standing still for you (don't worry about where their feet are yet--just that they aren't moving) begin sacking them out. I use a number of different things for this--usually first is kind of "jumping at them" which essentially is just moving at them quickly with my arms raised (have the lead in hand) and hissing at them (or make some other "foreign" noise--whatever suits you--try "BOO"). I do this slightly at first--all the while saying whoa to reinforce the lesson, and gradually "jump" at them more quickly, wilder arm movements, etc. Most of them will move the first time (so just use a firm steady pull and tell them whoa again), but (and I can't stress this enough--because you're trying to develop a learned response) as long as you DON'T HURT THEM in any way while you are doing it, they become pretty desensitized to it, and see that it's not going to hurt them, therefore they adopt the attitude of, "Oh well, this crazy human is just doing something stupid, BUT it's not hurting me, so I don't really care. "The same holds true with whatever you decide to personally use--whatever it is, fine, just DON'T let it hurt them, or they will not trust you when you tell them to whoa. I usually use a lunge whip, towels, the lead rope itself, a basketball, spray bottles--whatever. But you can use anything that you have that you think might normally make them nervous and use this as a way to get them accustomed to it so as not to be fearful.
I will twirl the lead to one side and over my head (and theirs) and let it make a whirring sound as it goes fast--all the while saying whoa. I will then use the end of the lead and lightly fling it at different parts of
their body and let it slightly "bump" them. Shoulders, over the back, all 4 legs, under the stomach, the butt--wherever--just don't get carried away and make it hurt. Same thing with the lunge whip--use it to scratch their belly (most LOVE that) then run it over their whole body--let it drape over their back and bring it forward to where you have to drag it over their ears and face--keep saying whoa. Use it off to the side and pop it (as long as you have enough control over it NOT to pop THEM with it) twirl it around--over their head, etc.

As you are doing this, don't forget to do it on BOTH sides of the horse. As long as you are out of the leading position, they are supposed to stand still. I have even bounced a basket ball off of my horses shoulders, sides and butt--but not hard enough to hurt--I moved in pretty close. You can use a towel to flap in the breeze or a saddle blanket, etc. Just remember to keep saying whoa and if they do move, get onto them about it. Use as much pressure as you need to make them stay back, and away from you.
That's the goal--plain and simple--no forward movement unless asked for, and when they do stand still, loosen the chain as a reward and pet them and praise their efforts. Some people may have the misconception that when you are pulling forward on the lead you are asking them to come forward. It doesn't work that way, as they learn to balance themselves and stay in "their space" by actually resisting the urge to go forward--learned response--that's what you're there for--to teach it to them.
Only after you can do all of this should you begin to set their feet--again, say whoa frequently as you get each foot set. When they have the idea about actually standing there (even before you set them up), use all the length of your lead (or lunge line) and step back away from them. If you walk straight away from them (with your back turned to them) they may try to follow the first time--firm pull and steady pressure, and of course, then say WHOA before and as you are walking away. Same thing goes for walking around the sides of them--give them the benefit of the doubt--give them slack in the lead but keep verbally telling them what you expect. I like to have them where I can put a lunge line on them and walk
forward as far as it will go (25-30 feet), and then walk around one side with it out that long, get to the back end, swing the rope and flip it over the horse's butt, to where I can walk on around to the other side, and then flip it over the horse's head. If it gets caught on their ears, all the better--it's just another desensitization exercise, and as long as it isn't hurting them, it won't scare them. This is how you go about teaching the ground tie. You give them plenty of slack, drop part of the lead or lunge line on the ground, and keep saying whoa. If you did your homework and taught the whoa to them, and didn't "baby doll around" with it, it will work for you, or anybody else. And yes, even if another horse flips over in front of
you--best chance is that the "jumping at them" that you did will be enough to keep those feet firmly planted on the ground. However the one thing you WON'T be able to do with them from this point
on is to haphazardly walk in front of them to "lead" them. You need to be specific and professional about how you lead them from that point on, which means you get into "the leading position" and cluck to then tell them that you want them to move forward. If not, most often they will "lock up on you" and go into "whoa mode" --so don't forget to be specific about what you really want. (And if you have taught this horse to whoa, and they actually do it when YOU aren't asking them correctly, DO NOT discipline them for behaving in a way that you taught them to behave!) Mixed signals aren't effective with horses--all that does is confuse them. Repetition of the correct way of doing things is the key. You are being responsible for their actions, by being responsible for yours.
Anyway, to me, a whoa is THE most important thing you can teach a horse---regardless of if it's going to be a show horse (halter horse or show trail ) or if it's just going to be a kids horse who needs to know to STOP when it is told to--whether to avoid stepping on the child or because the child is losing its balance, or if there is some kind of danger (foot caught in a fence, etc.). It's just something they need to be really solid on and understand.
    Another quick tip--once you have taught them to whoa, and you can put pressure on the lead (pulling toward you), it is VERY easy to work with their head position in a halter class. If you want it up high to tighten the underside of their neck, then pull forward and somewhat down (makes the head go up). If you want to stretch it toward you, pull forward steady, but also do small, gentle movements that help stretch the neck toward you--all the while saying whoa. Saying whoa is the one sure way to keep reminding them of what you want. Anyway, good luck everyone.

Commonly used Contracts and Forms:  (PDF Format)

Agreement for lease of a mare

Breeding contract

Liability statement

Sales agreement

Simple terms sales agreement