How appaloosa patterns work – part 1


I have some more pictures to post about appaloosa mottling and other characteristics, but before I do that, I thought it might be helpful to post some basic information about how appaloosa patterns work. Some of this information already appeared in The Boat magazine, but I’ll just take the parts necessary to give the basics. This has been a really exciting area of research in recent years, so there is a lot of information, but for now just the most important parts.

Prior Research and Assumptions

Earlier studies of the appaloosa patterns gave rise to a number of theories. One of the earliest was that blanket appaloosas were heterozygous, while leopard patterned appaloosas were homozygous. A later study by Dr. Sponenberg, done using Norikers, indicated that leopards were heterozygous while fewspots were homozygous. Varnish roan, which was not thought to exist in the Noriker, was not part of that study. It was assumed to be a separate pattern from the one responsible for leopard. Yet another study suggested it was possible to get almost any appaloosa pattern from any other appaloosa pattern.

Needless to say, the information that was available made for a confusing mess. For those that attended my color seminars and wondered why the appaloosa patterns were glossed over, this was why! None of the theories seemed to fit the actual situation, at least not well enough to inspire real confidence. How could a blanket horse produce a leopard, or a varnish horse produce a blanket? It seemed to me that researchers were missing something – something that could reconcile some (seemingly) contradictory theories.

The Missing Piece of the Puzzle

Understanding of appaloosa patterns took a huge leap forward with the work of Sheila Archer and the Appaloosa Project. Where older research on horse color (my own included) centered around studying the appearance of individual horses and trends within breeding groups, the Appaloosa Project was able to use modern gene mapping to better analyze information.

The missing piece – so often overlooked in early studies – was the varnish roan pattern. Far from being a separate, unrelated pattern, the Project researchers found that varnish was the key to all the other patterns.


The “Master Switch”

Color genes are often likened to on/off switches. What was discovered with the appaloosa patterns was that there was a “master switch”. This switch, when in the “on” position, made the whole range of patterns possible. If that switch was off (i.e., if that gene was not present), then none of the patterns were possible.

The gene itself did not create the patterns. Or rather, it created one of them; the one that had been ignored for so many years. The “master switch” for all the appaloosa patterns is the gene responsible for varnish roan. Underneath whatever other patterns are present, all appaloosas are varnish roans. This gene has been named “leopard complex”, which is usually abbreviated Lp. The name has lead to some confusion, since the gene is not directly reponsible for the leopard pattern. Instead, it sets the stage for the group (the “complex”) of patterns that includes – and is best known for – leopard.

So What Does the Leopard Complex Gene Do?

Leopard complex, or varnish roan, causes the coat to progressively lighten in a distinctive pattern. Typically a varnish roan will be lightest on the hindquarters, excepting some small spots on the hips, which are usually more densely pigmented than the body. The darkest areas (aside from the spots) appear along the high points of the body – the points of the hip and elbow, the outer edge of the barrel, the nasal bones, the ears – and the legs. The guy at the top of this post is a really good example to show where the varnish marks occur. His face is still dark now, but the beginnings of the classic “V” shape on the nasal bones can be seen in his face shot.

The leopard complex gene also creates what horsemen refer to as “appaloosa characteristics”. The mottled skin that was featured in the last post is on of those, as are striped hooves and visible sclera. It has often been stated that appaloosas will always have these three things, and that is true, though they are not always obvious – as the mottling pictures show. But they do have some degree of those traits because all appaloosa-patterned horses are (genetically at least) varnish roans.


What leopard complex does not do, at least not on its own, is add dense white patterning to the horse, nor does it add dramatic spotting. The louder, highly contrasting patterns so sought after by breeders are the result of other genes that work with the leopard complex gene.

Those genes that modify the varnish roan gene, and create the louder appaloosa patterns, will be the subject of the next post.

, , , ,

4 Responses to How appaloosa patterns work – part 1

  1. Ayla September 23, 2011 at 3:28 pm #

    Always excellent posts =D Is that first appaloosas bit on wrong??? It looks like it is backwards and not attached to the proper places!? I hope they got that fixed.
    I love this blog =) It is fun to read,has plenty of pics to explain and is very informative. Can’t wait for the book to come out =D

  2. The Equine Tapestry September 23, 2011 at 4:14 pm #

    I think by not attaching the cheek piece to the place on the bit for it, the pull on the ring caused it to flip over wrong. The second picture is of the same pony, and you can see the place where it should have been attached. I didn’t notice it when I was shooting (I’m usually too busy trying to stay out of the way and not get stepped on), but I did when I got home and was color-correcting the photos. Hopefully the folks connected to the pony were quicker to notice!

  3. Christine Sutcliffe September 23, 2011 at 5:10 pm #

    *steals reference pony*

    Appaloosa must be one of the hardest things to research as there’s just so many different variations of expression!

  4. The Equine Tapestry September 24, 2011 at 11:46 am #

    I agree Christine. It’s probably appropriate that they named in leopard COMPLEX. ;)