“A Puzzle Worth Solving”

Appaloosa Colour Pattern Transmission

Revised: Sheila Archer copyright 30/10/2002 ©

No portion of this document may be reproduced without the expressed written permission of the author.



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 that 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 White Appaloosa Pattern Gene (LP)

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 2, 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 2 have one LP gene. The level of white patterning is controlled by other modifying genes, some which enhance it, and others that damp it down. It is these genes that are the focus of my research.


What is a Homozygous Appaloosa?

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 1 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 have been 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 Cream 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.



What is the genetic status of a horse that has inherited no LP gene?

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 may 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!


Why Such a Wide Range of Colour Levels?

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.


But it’s not quite that simple, either – Base colour matters, too

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.

Putting it to the Test

The E-effect study that 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 that carry E (bay/black/darkpoint dun), and those that 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 is 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 that 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 working cow 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.



Mare & Foal Data – High Sign Nugget – Bay Fewspot with 90% White


Group 1 – Foals with Black, Bay or Other (E) Base Coats:


Chestnut mare (Reg. App) Black blanketed colt 60% white

“Ima Little Prescript”


Brown mare (Reg. App) Bay snowcap filly 50% white

“San Stone Image” Bay snowcap filly 40% white


Bay Mare (NC App) Bay filly with white hairs 5% white

“Ima Docs Doll” Bay blanketed colt 20% white

Bay blanketed filly 20% white


Black mare (NC App) Dark bay blanketed colt 60% white

“Texas Doe-C-Doe” Black blanketed colt 50% white


Chestnut mare (AQHA) Bay blanketed filly 30% white

“Fintry Little Zona” Black white-flecked colt 5% white


Black mare (Reg. App) Bay snowcap colt 40% white

“The Joker is Wild” Bay fewspot colt 80% white


Bay mare (Reg. App) Bay white-flecked colt 10% white

“S/W Red Velvet” Bay snowcap filly 70% white

Bay blanketed filly 20% white

Bay snowcap filly 70% white


Bay mare (NC App) Bay blanketed filly 50% white

“Ima Cody Olena” Black white-flecked filly 5% white


Bay mare (AQHA) Bay white-flecked filly 5% white

“Marglen Ms. Muffet” Bay blanketed colt 50% white




Bay mare (NC App) Bay leopard filly 80% white

“OK Top Doll”


Brown mare (Reg. App) Black white-flecked filly 5% white

“Doe’s Design”


Chestnut mare (AQHA) Black leopard colt 80% white

“Mighty Deck Charge” Bay blanketed colt 50% white


Black mare (AQHA) Black blanketed filly 60% white

“Juream Troupe” Black blanketed filly 60% white


Grulla mare (NC App) Grulla leopard colt 90% white

“Tip Top Topaz”


Black mare (NC App) Black white-flecked filly 10% white

“Screamin Lady Bug”


Chestnut mare (NC App) Bay white-flecked filly 10% white

“A Fantastic Dream”


Chestnut mare (AQHA) Bay blanketed colt 50% white

“Doc Sincs Tivio Rose”


Black mare (AQHA) Black characteristic colt 0% white

“Candy Cola”


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



Group 2 – Foals with Chestnut or Other Red (ee) Base Coats:


Chestnut mare (AQHA) Chestnut leopard colt 90% white

“Mighty Deck Charge”


Bay Mare (NC App) Chestnut blanketed colt 35% white

“Ima Docs Doll”


Black mare (AQHA) Chestnut leopard filly 80% white

“Cola Coka”



Bay mare (AQHA) Chestnut leopard filly 80% white

“Marglen Ms. Muffet”


Chestnut mare (Char App) Chestnut leopard filly 80% white

“Ima Little Prescript”


Chestnut mare (NC App) Dark palomino filly 80% white

“Ms. Dazzlin Gem”


Black mare (NC App) Chestnut near-leopard filly 70% white

“Screamin Lady Bug”


Palomino mare (NC App) Chestnut leopard colt 90% white

“A Rumor Hasit” Palomino leopard filly 90% white

Chestnut mare (AQHA) Chestnut leopard filly 90% white

“Lady Siemon Bee” Chestnut leopard filly 90% white


Chestnut mare (AQHA) Chestnut near-leopard filly 70% white

“Liebchen Seven”


Chestnut mare (AQHA) Chestnut leopard colt 100% white

“Fintry Little Zona”


Chestnut mare (Reg. App) Chestnut near-leopard filly 70% white

“Ima Jessalena” Chestnut leopard colt 90% white


Brown mare (Reg. App) Chestnut near-leopard colt 70% white

“Star Dawn Bonanza” Chestnut leopard colt 90% white


Seal Brown mare (NC App) Chestnut leopard colt 90% white

“Sweet Sonita” Chestnut leopard colt 90% white


Black mare (NC App) Chestnut near-leopard filly 70% white

“Bright Eyes Spirit”


Bay mare (Reg App) Chestnut near-leopard filly 70% white

“SW Red Velvet”


Red-based (ee) Foals Average White Level = 80% 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.

What does the E-effect mean to Appaloosa breeders?

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 phaeomelanin, 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 that 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.


The Next Step – Exploring White Modifier Math

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 each other 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.


Choose it or Lose it

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.


Five steps to take to avoid depleting the Appaloosa breeding stock of heLPful white pattern modifiers and keep them plentiful in the gene pool:


-         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