The following appears with the permission of The Appaloosa Project, as a series of Questions and Answers from The Appaloosa Project Classroom, November 2010.

Leading researcher, Sheila Archer, is responding to questions regarding the LP gene.

(Questions are shown in italic blue text.)

Visit the Appaloosa Project website to learn more.

Thank you for your questions about LP and various paint pattern causing mutations. This is a long answer, as your questions require a lot of explanations. Please write back with any additional questions you may have after you've read my response!

You wrote:
You have said that the LP gene is also present in other breeds.. mustang and spanish horses etc.. AQHA are heavily crossed along those lines.. so would it be right to assume that the LP gene is present in most any of the modern horses?

Quarter Horses do share common ancestry with the Appaloosa, as both breeds are believed by researchers to trace back to LP-carrying Spanish Mustangs. Given this it is not surprising that in spite of past efforts on the part of the AQHA to weed out LP-carrying horses, there are some known examples of LP-carrying Quarter Horses living today, but they are very rare.

How can this happen, when we know that the LP mutation is dominant? While it is true that, if a horse has inherited it, LP-caused traits (called "characteristics") will be expressed. However, the intensity of the expression of mottling, striped hooves, etc. may vary, with a few horses showing extremely minimal signs that LP is present.

Knowing this, we say that LP cannot truly hide, but that under certain conditions it can be difficult to detect (of course, with the advent of a DNA test for LP, these "maybe" horses can be figured out now).

More about "late bloomers": In some horses, LP-caused traits are not present at birth, even though LP has been inherited. As the horse matures, they gradually appear, but in extreme cases, the mottling, hoof stripes and Appaloosa roaning are so minimal that the horse can "pass" as a normal roan.

This is probably how LP stayed in the QH gene pool. These "late bloomer" cases are usually female, and they can take many years to develop to the point where someone might suspect LP is there. Not knowing what they are seeing, a QH breeder might just ignore them. Or, they might know, but since the horse has papers already, they'd be inclined to say nothing.

I will add that LP can also be masked by the presence of grey (G) or classic roan (Rn). So, if a QH breeder was working with bloodlines that also contained one of these, LP would have a chance to hide... but only for a while.

Sooner or later, a foal is going to be born that, according to the old AQHA rules, is not registerable. Nowadays, an obviously blanketed foal can still get AQHA papers. Before the rule change, these horses were quietly sold off.

Would the LP gene be responsible then for the excessive white/paint pattering that showed up among AQHA leading to the paint registry?

Definitely not - the LP mutation and the various paint pattern causing mutations are totally different from each other. LP does not cause paint patterning. The excessive white patterning you are referring to is most likely being caused by either the frame overo mutation, a form of sabino (more than one mutation) or the splashed white mutation (there may be more than one of these, too).

The tobiano mutation has probably been totally weeded out from the AQHA gene pool - the descendents are now in the various Paint registries.

The paint mutations that still exist in the QH breed are difficult to remove completely, which is probably why the AQHA changed its rules. Frame overo, splashed white and the various sabino pattern causing mutations can be present, yet so minimally expressed that the horse can "pass" as a non-paint. These same paint causing mutations are also present in the Appaloosa, and thus cause the same problems there.

Paints have similar traits as appaloosas, striped hooves and white sclera.

Yes - but LP is an apple, and the various paint causing mutations are each other types of fruit, every one of them unique. What they have in common is the ability to affect how much pigment is expressed in the sclera and the hooves - that's all.

If you have a solid paint or appy with just characteristics the only difference is mottled skin vs no mottling?

A solid Appaloosa that has "characteristics" has inherited LP. Paint horses with mottled skin have inherited other mutations that affect the pigmentation of their skin - they are not comparable genetically, and the physical similarity is superficial.

We know the appaloosa patterns are appaloosa .. but are there also sabino, overo and frame genes present as modifiers along side appaloosa or are the two distinctly different and those genes, if found in an appaloosa, only the result of paint x app crosses at some point eg Old Fred line? I know of horses that are app x app for 6 generations to Old Fred that has the bald face and high whites.

As mentioned above, splashed white, sabino mutations and even frame (low but there) are all present in the Appaloosa gene pool. It is simply not possible to get them all weeded out - they've been there a long time, and there's lots of them. Also, Old Fred is probably not the only source of splashed white.

As for interactions with LP, we do believe that some sabino-causing mutations may interact with LP. The interaction seems to result in the horse having louder/more extensive white Appaloosa-type patterning than a horse with little or no face or leg markings (Archer, unpublished phenotype data). In other words, some forms of sabino may act as PATN modifiers with LP.

In contrast, we don't have any conclusive data, phenotype or genotype based, to suggest that tobiano, frame overo or splashed white act this way. Until there's a DNA test for splashed white, we can't pursue this further.

The fact that there are still splashed white descendents of Old Fred in the Appaloosa gene pool is not surprising, since the Bright Eyes Brother bloodline is very popular. It's also extremely hard to remove splashed white from a breed. It "hides" at a very low level of expression in some horses, only to jump out "loud and proud" when the right combination of factors comes together in a subsequent generation.

LP may or may not interact with splashed white - we don't know. But we do know that these are two different mutations, very likely inherited independantly.

Would this horse's parents both have to go back to Old Fred in order to have produced the characteristics? I would assume the genes be recessive and it take two copies of the gene to be expressed.

No - only one parent need trace back to Old Fred. A very loud splashed white plus Appaloosa foal can occur if the splash mutation comes together with the right modifiers. When it gets what it needs, it goes loud, and the resulting foal may not be registerable.

If there are modifiers in the Appaloosa gene pool other than LP that help this splashaloosa effect to happen, we don't know yet what they are. The best strategy for minimizing the chances of this happening is to avoid crossing horses with known splash marked offspring to horses with extensive sabino markings. Sabino does appear to have an enhancing effect on splash...

Hope this helps!
Sheila Archer

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Three SNPs in very close proximity to the LP mutation have been found, such that DNA testing for LP can now be developed. Read the article below, on the Appaloosa Project site: The LP SNP Discovery

The Appaloosa Project is an international collaborative effort by scientists interested in unravelling the mysteries of pigmentation in the horse. The goal of the project is to identify and isolate the main genes responsible for Appaloosa patterning, and to investigate key physical traits associated with these genes.

The Appaloosa Project is dedicated to unravelling the genetic truths that govern Appaloosa coat patterning. The information they provide is backed by research that meets the rigorous standards demanded by the scientific community and/or can be proven by DNA tests performed by recognised laboratories.

We encourage you to subscribe to the Appaloosa Project: as this provides members with a unique opportunity to obtain information first hand from its research team. If the co-ordinator and chief phenotype researcher for the Appaloosa Project is not the person who is best qualified to answer your question, you'll receive an answer from the person who is - including molecular biologists and veterinary ophthalmolgists.

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LP (leopard complex) & PATN Color in Quarter Horses