November 2011

I have had a number of people contact me asking about the color on this mare, currently with the Another Chance 4 Horses rescue. I apologize to those easily upset, since these are photos of a horse in obvious need of a more caring owner. I do want to talk about her coloring, though, because horses like this are often misidentified. I’d love to see her find a good home with someone who would feed her properly, but I also think that all animals are more likely to find permanent homes when the people around them understand what they are – and what they are not.

Horses with this kind of coloring have occurred in the past, and in the case with the most concrete information, it was believed to be the result of a fungal infection. That was the WC Saddlebred Simply Striking. Here is a picture of Simply Striking as he was before the condition. Here is one from after the infection, where he shows a strong resemblance to the rescue mare. In later photos, the white areas are far less distinct, which suggests that some of the hairs later come back dark again. The discolored areas also appear to have spread, though whatever has been used to treat the infection might play a part in that, too.

If infection is part of this type of color, that is important to know because that would place horses like this mare into the same category as horses with somatic mutations. That is, they are “cool colored horses that didn’t come from cool colors and will not themselves produce cool colors.” This is important because historically horses of unexpected colors were hidden, so as not to reflect poorly on the breeding programs that produced them. In some cases, perfectly good horses were culled from breeding just for producing a horse of questionable coloring. The tables have turned somewhat in recent years, so that horses are now more desirable (at least to some) for their unusual colors. That puts horses like this mare at risk for ending up homeless again, since someone looking to recreate the pattern is likely destined for disappointment.

The other problem is when the pattern is mistaken for something else. It seems most often horses like this end up misidentified as appaloosas. Here is a purebred Thoroughbred mare, Pelouse’s Queen, with a similar pattern.

She was part of the Money Creek appaloosa breeding program. In the 1970s, when she was of breeding age, good Thoroughbred mares were in demand to improve the Appaloosa breed. The idea that they could contribute color as well, and lessen the chance of a solid foal, would have been very appealing. In today’s market, it is not hard to imagine someone purchasing a mare like Pelouse’s Queen with the idea that they might be able to found a line of purebred “appaloosa” Thoroughbreds. If her pattern, like the one on Simply Striking, was the result of an infection, then she would be no more likely to pass along color than any other brown Thoroughbred. (Whether she might have a genetic predisposition to recurring fungal infections might be another issue entirely!)

The mare pictured at the top was listed as a “pintaloosa”. In all likelihood, she doesn’t have either a pinto or an appaloosa pattern and would probably breed like an ordinary chestnut mare. Like horses with somatic mutations, she truly is unique. Hopefully she will find a home with someone who appreciates her.

[Note: there is a link to another horse like this in the comments section, and I am hoping to post some more detailed shots of yet another horse in the near future.]

I apologize for the silence on the blog, as well as the delays in my responses to those of you who have sent me emails. My desktop computer has had some hardware issues that have made it unstable for a while now, and the other night it finally gave up the ghost. Nothing significant was lost – I certainly had plenty of warnings that backups would be required! – but I did decide that it was time to switch platforms. It will take me a little while to get everything set up on the new system, so it might remain quiet here for a few more days.

I have high hopes that this switch will allow me to finally get the first book out the door. At close to 400 pages and filled with hundreds of photos, illustrations and charts, it has been a strain for my old computer to manage. I have been losing a depressing amount of time battling computer problems, but I have been stubborn about changing midstream. Too bad I had never seen a Magic Trackpad before, or I might have gotten over my stubbornness a lot sooner!

It has been exciting to see that the recent paper on horse color and cave art has gotten a lot of attention in the mainstream press. It is great to see scientists like Rebecca Bellone, the lead researcher from The Appaloosa Project, recognized for their work. I also love the idea that an area of study traditionally connected with agricultural and veterinary science could be used to better understand seemingly unrelated fields of archeology and art history. It makes sense that in understanding the horse, whose history is so intertwined with our own, we gain insight into ourselves.

That is the larger picture. From the smaller picture that is the focus of this blog, the study offers some big surprises.

To adequately explain, I’ll need to expand on the comments that were made in the earlier post on gene locations. In 2009, the paper “Coat color variation at the beginning of horse domestication” was published. In that study, ancient remains were tested for the presence of color mutations. The range of tests available at the time included:
Extension (black/red)
Agouti (bay/black)

Those tests determined that all but the frame gene were present among the early domesticated horses. That is certainly in keeping with the theory that frame is a New World mutation. It also showed that in the wild populations – horses living somewhere between 15,000 and 3,100 BC and predating domestication – the only mutation was black. Black horses were found among the wild populations in Romania, Ukraine and the Iberian Peninsula. The other populations, which included remains from Siberia and Germany, were entirely bay.

The two patterning genes, Tobiano and Sabino1, were found in remains of domesticated horses. That is in keeping with the idea that spotting mutations are linked to selection for tameness. The Russian Farm Fox study is often cited as a good example of this, but most people familiar with newly introduced “pocket pet” species have seen this in action. It usually doesn’t take long after a species becomes popularized before spotting patterns begin to appear.

What makes the cave painting study so fascinating is that the appaloosa patterning gene was found in a wild population. And it wasn’t just one horse. Of the thirty-one samples, six were carrying the mutation for leopard complex (Lp). Were someone to assemble a random sampling of modern domestic horses, it would be unusual to say the least to find that kind of ratio of appaloosas to non-appaloosas.

Also interesting is the fact that while there were six leopard complex horses, there were no chestnuts. Chestnut is found in the Przewalski Horses, where it has been documented as far back as the early twentieth century in skins taken in Mongolia. In the cave art study, there was a single Romanian sample that tested as carrying chestnut, so the mutation did exist at least in that population.  It would seem to be rare compared to leopard complex, and not nearly as old. The German samples with leopard complex date between 15,000 and 11,000 BC, whereas the Romanian with the chestnut allele is 4,300 BC. This is interesting when one considers how in many primitive European pony breeds, chestnut is non-existent, or when found is considered proof of foreign influence. It also gives a certain level of credibility to claims made by both Gypsy Cob and British Spotted Pony breeders that appaloosa coloring was once part of the native population.

It is also interesting that this mutation occurred in a wild population, and was obviously perpetuated, despite the fact that homozygous leopard complex horses have a defect. They are blind in low-light situations, which should act as a negative selection factor. None of the horses tested as homozygous for leopard complex.


As exciting as the results of the study are, some limitations have to be remembered. Probably the most important is that this was a really small sample set. Getting usable genetic material from ancient remains is difficult, which is why there are only 31 samples. Broken down by time frame and geographic location, you end up with even smaller groups. These tests can certainly confirm that a mutation was present, but it is hard to draw any firm conclusions about the whole of the ancient horse population based on so few animals.

We also only have a partial picture, because we only have a partial set of color tests. The previous study, done in 2009, used some of those same samples. Without the leopard complex test, which was not yet developed then, we only knew that the wild horses were bay or black. With the new test, we now know that, yes, they were bay and black – and some where varnish roans (leopard complex). We don’t yet know if they had the patterning genes that turn leopard complex into true leopard patterns, though certainly the cave paintings would suggest that this was so. Likewise, we assume that the original horses were dun, since that coloration is associated with wild equines, including the last remaining wild horse. A completely reliable test for dun is not yet available, so that part of the picture is incomplete as well. Those bays and blacks, now known to in some cases be bay or black varnish roans, may later prove to be dun and grulla varnish roans – or not!

We know they were not silver or cream, since those can be and were tested. But as new color tests are developed, we may later learn that some of those horses were also roan or grey or splash. It may be that varnish roan will eventually lose its place, but for the moment it is the oldest tested pattern.

I mentioned in a previous post that both Sabino1 and Tobiano were really old genes. The paper detailing that study was among the most fascinating articles on horse color that I had read in recent years. Now there is a new study out that shows that Leopard Complex, the gene responsible for setting up the various appaloosa patterns, was present far earlier than anyone expected.

The dappled horses’ spotted coat pattern bears a strong resemblance to a pattern known as ‘leopard’ in modern horses. However, as some researchers believed a spotted coat phenotype unlikely at this time, pre-historians have often argued for more complex explanations, suggesting the spotted pattern was in some way symbolic or abstract.

Researchers from the UK, Germany, USA, Spain, Russia and Mexico genotyped and analysed nine coat-colour loci in 31 pre-domestic horses dating back as far as 35,000 years ago from Siberia, Eastern and Western Europe and the Iberian Peninsula. This involved analysing bones and teeth specimens from 15 locations.

They found that four Pleistocene and two Copper Age samples from Western and Eastern Europe shared a gene associated with leopard spotting, providing the first evidence that spotted horses existed at this time.

The full article can be read here.

As more and more tests become available for the different colors, it will be interesting to learn just how old some of them are.

(Thank you to Jackie Arns for the lead on the study!)

This horse has one copy of the frame mutation. Horses with two copies of the mutation are not viable.

In the previous post I talked about how the physical location of a mutation can limit the possible pattern combination. There is another potential limitation, which is viability of the organism.

Those of us that like horse colors, particularly the white patterns, are accustomed to thinking of colors as something that is added to what would otherwise be a horse of ordinary coloring. So the horse above has white markings on his body in addition to his chestnut coloring. That is certainly how a lot of artists would approach painting such a horse.

But from a genetic standpoint, that’s not what has happened. Generally speaking, white patterns result when one of the genes involved in pigmentation is impaired. Something prevents the normal function of the gene, and as a result pigment is not distributed in the normal fashion.  That is what we see most clearly, because changes to coloration are really obvious. But those same genes do not just regulate color, and those other functions may be effected as well. Hampering coloration is largely cosmetic, but altering the function of the gene can have more serious implications.

That’s why horses with two copies of the frame mutation are not viable. With just one impaired gene, the horse is not completely pigmented (ie., it has white patches) but is still functional. The horse still has one non-mutated copy of EDNRB, the gene involved with the frame pattern. It can “pick up the slack” for the necessary functions that gene performs. When the horse inherits two copies of the mutation, there is no backup and the gene cannot perform its function in the development of the embryo. In this particular case, no pigmentation occurs, which is why the resulting foals are white, but more importantly the colon is incomplete which means the foal cannot survive.

Lethal White Syndrome is probably one of the best known problems with color because it involves the heartbreak of a live birth of a foal that must be humanely euthanized. Other colors, most notably the various forms of Dominant White, are also thought to be lethal when homozygous. Like the frame mutation, two copies impair the function of the gene to the point that the embryo is no longer viable. The difference between Dominant White and Frame Overo is that the embryo is lost early enough that no foal is born. This may explain why programs centered around breeding white-born horses in the seventeenth and eighteenth century were often plagued by infertility issues.

At one time, roan was also thought to be a homozygous lethal. (Photo from Wikimedia Commons.)


In the past, before tests were available, lethal conditions like this were determined by analyzing production numbers. If the ratio of mutated to non-mutated offspring was off, and if true-breeding individuals could not be found, the trait was suspected of being lethal when homozygous. That was why roan was assumed to be a homozygous lethal for so long. Initial studies of production records showed that the ratios of mutated offspring were like those of a homozygous lethal, rather than a simple dominant. Proven homozygous roan stallions have since been identified, so it is clear that two roan genes are not always lethal, at the very least.

So what does this have to do with the KIT mutations? In the comments section, there was speculation of the last post about whether or not mutations could crossover, resulting in a single gene with two separate mutations, rather than two separate genes with one mutation on each. Not asked, but an equally valid question, is whether or not a gene that already contained a known mutation could mutate again. If either were to happen, the next question would be could the situation result in a viable embryo? Would the added layer of impairment change the coloring, or would it damage or even destroy the organism? Have we not yet seen a horse with three KIT mutations (one on one gene, two on the other) because the statistical chances are infinitesimally small, or because the function of some gene is too compromised to result in a viable embryo?

I have wanted to bring up a more technical aspect of horse color for a while, but have struggled with the best way to present the information. Part of the problem is that the way we talk about horse color is misleading. For this to make any sense, I will have to clarify some terms.

We often talk about horse colors as if they are genes. We say, then, that a horse like the one pictured above has one copy of the “sabino gene” and one copy of the “tobiano gene”. It is true that the “torn tissue” look to his pattern is very typical of what a horse looks like when it has both Sabino1 and Tobiano. He is a Spotted Saddler, so he would likely test positive for each color. Saying he has the Sabino1 gene and the Tobiano gene is a simple way to get that idea across.

The trouble is that there is not a specific Sabino1 gene. There isn’t a Tobiano gene. Sabino1 and Tobiano are mutations of an existing gene. When we say that a horse has the “tobiano gene” or the “not-tobiano gene”, what we really mean is that the gene that was there from the start is either mutated (tobiano) or not mutated (non-tobiano). This makes sense when you think about it. Why would an organism carry around a gene that is essentially the absence of a trait?

This might seem like semantics, except that some of what we think of as separate colors occur on the same actual gene. They are different mutations, but they share a location. In the case of Sabino1, the mutation occurred on a gene known as KIT. Other mutations found on or very close to KIT are tobiano, true roan and dominant white. This might not seem important until you remember that an animal has two copies of any given gene, one from each parent. It can only give one to any individual offspring. If a horse only has two KIT genes, then it can only carry two mutations – one on each copy of the gene. That means you only have two slots to fill with KIT mutations. A horse could be homozygous for tobiano, but then he could not also carry Sabino1. His two KIT slots are already filled.

This probably makes more sense when it is understood that most color mutations are one-time events that happened a very long time ago. Sabino1 has been documented in Siberia in the early Bronze Age, so it is at least that old. Horses like the one pictured here descend in an unbroken line from whatever early ancestor carried that first Sabino1 mutation. One of his KIT genes is that same gene with that same mutation. His other KIT gene comes from the whatever horse carried the first tobiano mutation. That pattern has been found in Eastern Europe later in the  Bronze Age, so like Sabino1 it is really old. Were he not a gelding, he could in turn pass on one of those – either tobiano or sabino1 – to his offspring. One, but not both.

This has implications for artists like myself because we tend to mix-and-match the details of different patterns to get certain visual effects. What we have to be careful about is whether or not the limitations of gene locations make something impossible. If a horse can only carry two KIT mutations, and true roan and tobiano prove to be on KIT or linked to KIT, then is a homozygous tobiano roan possible? Is a roan tobiano with cat track markings – a trait closely associated with homozygosity in tobianos – accurate? And what about the other colors and patterns that have not been mapped to a specific location? What conflicts will become apparent when more mutations have known locations? We know, for instance, that the leopard complex gene (varnish roan) is not located on KIT, but what about the patterning genes that work with leopard complex to make the more vivid appaloosa patterns? It is often assumed that all combinations are possible, though they might be so rare that actual living animals cannot be found with them. That is probably a mistaken assumption, with some combinations not possible because of location conflicts.

This also has implications for people who study horse color. Homozygous tobianos are an interesting example because they obviously have two KIT-related mutations. Still a high percentage of homozygous tobianos have face markings. The commonly accepted wisdom is that tobiano by itself will not place white on the face, yet KIT is often assumed to be involved in ordinary face markings as well as the sabino patterns. Does the fact that many homozygous tobianos have broad blazes suggest that some sabino patterns are not, in fact, located on KIT? Or does it suggest that in its homozygous state, tobiano does start to place white on the face?

It is also important to breeders, who may find that attractive combinations do not necessarily breed true. Many Paint Horse breeders have already noted this situation with roan tobianos. Roan has not yet been definitively mapped, and it is thought to be close to KIT rather than on KIT. Still genes that sit close to one another tend to travel as a package, and that is definitely the case with roan and KIT. Roan tobianos typically have a roan parent and a tobiano parent, and they usually pass along either roan or tobiano to their foals, but not both.

Gene location is pretty technical stuff, but the information has a lot of practical uses.

I have one last variety of roaning to share. The mare in these photos is a Quarter Horse, and is what is often called a frosty roan. Like true, dark-headed roans, frosty roans have white hairs mixed in a dark coat, but unlike the true roan the hair is not evenly distributed. Instead it tends to concentrate more heavily on the topline, including the mane and tail.  On a true roan, the mane and tail remain dark.

There are also concentrations of white hairs where the bones are more prominent. It’s hard to see because of the shadows cast by her saddle, but notice the pale area over her elbow. This can be seen on her hocks, too.

She also has white hairs along her nasal bones. (I suspect the small white patch on the right side is a marking, and not part of her roaning.)

In this way, frosty roans display the opposite pattern of white hairs than a varnish roan, which tends to retain color across the bony ridges. Here is a varish face with dark nasal bones and roaning on the rest of the face.

Varnish roans typically have paler hindquarters, but the other areas where a frosty would be pale, a varnish tends to be darker. Here is the body of a varnish roan, showing how the jaw, elbows and the hocks are darker.

There has been speculation that the gene that causes frosty roaning, paired with true roan, may be responsible for the very pale manes and tails on some of the European draft horses. Among those breeds, black, brown and bay roans often have markedly silver manes and tails. These are often more dramatic than the ones seen in ordinary frosty roans like the Quarter Horse above. That may be because the two genes interact, or it may be that the two are similar, but genetically unrelated. (The Brabant pictured comes from Wikipedia.)

It is not unusual for visually similar colors, like roan and frosty roan, to end up combined in a population. When breeders find a given color appealing, there is often a bias towards selecting horses that have that color – or something that looks a lot like it. That is how breeders of “golden” Saddlebreds ended up with both champagne and palomino horses in their breeding programs. Having two (or more) different genes that produce similar effects can also increase the chance that foals have the desired color, because each gene is a separate chance to get the desired look. Unfortunately for those interested in horse color research, it can also make sorting out the underlying causes a lot harder.