Basic Genetics


This is a good video explaining chimerism. It deals with cats and human beings, but the general concept is the same for horses. (Thank you, Joanie, for sharing it!)

I sometimes get asked why I do not often discuss brindles. A large part of it is that, as a fraternal twin myself, I find the type of chimerism responsible for brindle in horses – called tetragametic chimerism – deeply disturbing. There are other forms that do not involve the fusing of two embryos into one organism, as the video explains. The video talks about microchimerism, where genetic material passes from the fetus to the mother. There is also blood chimerism, where genetic material passes between twins through a shared portion of the placenta. A certain portion of fraternal twins are blood chimeras. Because I have had a conflicting blood type test in the past, and because my twin had a different blood type, it is possible that I am part of that group. (It is also possible that I had perfectly ordinary blood and a careless individual performing a blood test.)

In yesterday’s post I mentioned that breeders have a new way of finding closely related breeding groups. Genetic markers allow scientists to map out the relationships between the different breeds. This type of analysis was how the Abaco Barbs were identified as belonging the the Colonial Spanish breeding group. This can be really useful for feral herds like the Abacos where there are conflicting theories regarding the origin of the horses.

It is also being used to identify unique populations, with genetically distinct profiles, to target for preservation. This was recently done with a relatively large group of French breeds. The study is open access, so it can be read here:

Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

Studies like this can turn up surprising results. In this particular one, the distance between two breeds that many would have assumed to be closely related – the Percheron and the Boulonnais – were actually quite distant. Both breeds are large, grey drafters from the same part of the world. Some historical accounts even suggest that the latter was used to create the former. And yet the Percheron is more closely related to the Norman Cob (technically a light breed) and the stout, silver dapple Comtois than to the Boulonnais. Here is a chart from that paper showing one method used to group the breeds studied.

Breed legend: PS - Thoroughbred, AA- Anglo-Arabians, SF - Selle Francais, TF - French Trotter, APPAL - Appaloosa, QH - Quarter Horse, AR - Arabian, LUS - Lusitano, PRE - Pura Raza Espanol, AB - Arab-Barb, BA - Barb, LAND - Landais, CAM - Camargue, POT-Pottock, PFS - French Pony, CO - Connemara, WAB - Welsh Pony, NF - New Forest, MER - Merens, BR - Breton, COBND - Norman Cob, COMT - Comtois, PER - Percheron, HAF - Haflinger, POIT - Mulassier, ARD - Ardennais, AUX - Auxois, TDN - Trait du Nord, BOUL - Boulonnais, FRI - Friesian, FJ - Fjord, SHE - Shetland, IS - Icelandic, PRW - Przewalski

Results like this challenge some of our assumptions about breeds. The authors of the study note that a few of the breeds clustered in groups that are different from French registry classifications. Those appear in italics on the chart. The Camargue, considered a warmblood breed in France, falls into the pony breeds, while the Merens, Halflinger and Friesian all cluster with the draft breeds. (To be fair the Friesian is a bit of an outlier there, as it is in almost any equine relationship chart.)

Sometimes the results of these kinds of studies vary a bit in the details, depending on the specific samples used (this one used a pretty large set) or the specific markers being studied. Others are really consistent from study to study, like the grouping of Nordic breeds, highlighted here in pink.

Of course, it is heresy in many Fjord and Icelandic circles to suggest that these horses are ponies. For that matter, the other group that falls into this same cluster (although not used in this study) is the Miniature Horse, which many admirers adamantly insist is not a pony either. Of course, it is hard to maintain that position when your closest relative is the quintessential pony, the Shetland.

Swapping the sections of the chart around, though, shows that the graphs for these Nordic breeds look more like the section of the graph for the other ponies than for the light breeds. Those are the breeds most Americans imagine when the word horse, and not pony, is used.

This is still really new science, but these kinds of papers have been appearing with increasing regularity. Hopefully they will one day provide an even clearer picture of how the different breeds developed and are related. But even with what we know now, it is possible to make more educated guesses about what needs to be preserved, and what might be the best path to take for those breeds with limited numbers. The new information will probably require that we lose some of the mythology that has surrounded many of our breeds, but the benefit should be healthier horses in the long term.

(Fjord image from Mirk-Stock and used with permission, original chart from the open access paper linked in this post.)

The conversation over the last few days regarding pintaloosas reminded me that it might be helpful to talk about epistasis.

Most people are familiar with the idea of dominance. Dominance describes the relationship between versions (alleles) of the same gene. The gene responsible for greying (G), for instance, is dominant to the one for not greying (g). Dominance is often misunderstood to mean prevalent, as in “the dominant color in Morgans is chestnut.” In those cases it is probably a lot less confusing to say a color is predominant in a breed, rather than dominant. All the chestnut Morgans in the world cannot make chestnut a dominant gene!

The term dominance is also misused to describe how genes interact with unrelated genes. Grey is again a good example, because it is probably the most common gene spoken of in this way. It is not unusual to hear “grey is dominant to all the other colors.” It is not; grey is only dominant to not-grey. The relationship grey has to the other colors is what is known as epistasis.

Epistasis describes the situation where the actions of one gene hide the actions of another unrelated gene. Grey is not dominant to the other colors, but it is epistatic. It eventually hides the colors and patterns the horse has. Chestnut is the very bottom in terms of dominance, because it is recessive to the black-based colors. But it is also epistatic, because the gene that controls where the black goes (ie., whether the horse is bay or black) cannot be seen on a chestnut horse. There is no black to show which version a chestnut horse has, so those instructions are hidden. They are, however, still there. That’s why the right chestnut horse, bred to a black horse (recessive to bay), can produce a bay foal. It was carrying the dominant bay gene, hidden by the actions of its recessive red gene.

The mare pictured above is another example of how epistasis can work. She is the chestnut Morgan, Amanda’s Suzie Q. As the link to her web page shows, she carries the silver dilution gene. She was one of the earliest identified silver carriers in Morgans. The color doesn’t show on her because silver dilutes black pigment. Since Suzie doesn’t have black pigment, the effects of the silver gene cannot be seen. Silver is a dominant gene, but it just doesn’t have anything to work with on Suzie. It was visible on her bay foals, though, which is how she came to be identified. (Suzie was also instrumental in disproving the idea that silver at least lightened the manes and tails of a chestnut, since she has a self-colored mane and tail.)

A very similar situation exists with the cream dilution. Just as silver only dilutes black pigment, cream only dilutes red pigment. Here the epistatic color is black, because there is no red pigment to dilute. This horse is a black Foxtrotter named Quick Trigger. He carries the cream gene hidden by his black coat. Cream is not hidden because it is recessive, but because the genes that made Trigger black set up a situation where the cream could not be seen.

Or perhaps a better statement would be “could not easily be seen”. In many cases epistatic relationships, while they hide the actions of a gene, don’t necessarily make it impossible to see the effects. Sometimes they just make it pretty difficult, or difficult to be sure. Some blacks with the cream gene look more faded than those without it, for instance. Unfortunately for people wanting to identify them visually, though, quite a few blacks without cream fade pretty badly.

That is what was happening with the pintaloosas and the grey appaloosas. Generally the more white the horse has, the harder the individual patterns are to identify. We can guess, based on what is found in a given breed, and what traits are most typical of this or that pattern, but without tests it can be hard to be sure.

Here are some shots of the horse used in the post to illustrate the difference between cremello and truly white skin.

Those were his colored areas, while the rest of him was white. (I was never in a position to get a good shot of his whole body, unfortunately.) He was also a rescue horse, so nothing much was known of his background.

You could overlay a typical tobiano pattern on a horse like this and not see it. Does that mean he is a tobiano? Not necessarily, since you can layer mutiple overo patterns and get that much white. There isn’t any way to know without testing. Whenever people breed a lot of different color genes together, things tend to get muddied like this. It often makes for very cool looking horses, like the ones in the last few posts, but it sure can make it hard to be sure what genes they carry.

Although it’s not about horse color, polydactyls are fascinating in terms of genetics. Here is a good blog post about them, complete with a radiograph that shows where the extra digit originated.

Polydactyl People and Ponies – A Gallery of Extra Digits (and Hooves)

My youngest son is an avid video game player, so he was highly amused to learn that one of the genes involved in limb development – and therefor in polydactylism – is called Sonic Hedgehog (Shh). Here is a good article on Hemingway’s polydactyl cats that explains the hedgehog genes.

For Whom the Cell Mutates

(The zebra photos in this post all come from the Wikipedia site.)

In the previous post I mentioned the curious fact that zebra hybrids had more stripes than their zebra parent. So how does an animal with some stripes, bred to one without any at all, produce offspring more extensively striped?

According to the theory offered by developmental biologist Jonathan Bard, it’s all about the timing. The amount of striping depends on when the pigmentation initiates during embryonic development. The interval of striping is the same in each species – he postulates every 20 cells – but starting earlier means there are fewer cells. Alternating colors every twenty cells won’t give you quite so many stripes. That is why the Burchell’s Zebra has such sparse, but broad, striping. It is estimated that striping here began 21 days into development.

If you wait a little longer, when the developing fetus has more cells, that same 20 cell interval will give more stripes. This is a Mountain Zebra, with stripes estimated to start at 28 days.

And finally there is the heavily striped Grevy’s Zebra, with striping initiated at 35 days. That late in development, when the fetus was made up of many more cells, the twenty-cell interval created a lot more stripes.

This theory could explain why a hybrid might have more stripes than the parent. It wouldn’t need a genetic mechanism to tell it to make more stripes; it just needs the mechanism already there to be delayed a little. That is the part about zebras and their striping that has implications for horse color. If this can work for striping, it could work for other forms of patterning. It might not be necessary for a horse to have some genetic component that said “make more spots”. All that might be needed is something that set the stage for those spots to start later in development. Certainly this situation calls to mind the kind of changes in spot size and frequency seen in horses with some types of sabino patterning.

For anyone interested in a more detailed explanation of Jonathan Bard’s theory, this post has a detailed but still easy-to-understand explanation. I would also highly recommend the book that first alerted me to it.

For those interested in animal color, the chapter “Paint it Black” is great reading. But mostly about how advances in genetics and embryonic development have shed new light on the theory of evolution. I found it fascinating and very readable, even if he did talk too much about bugs for me. (I am horribly bug phobic!)

When you hear hoofbeats, think horses, not zebras


I have been thinking about zebras lately. Part of the reason is probably best left for another post, since it’s a different tangent than this one. As readers of the studio blog know, I tend to wander off on tangents a lot. I do eventually get back to where I was, though it often takes a while. Oddly enough, this will bring us back to Dominant Whites, though a bit indirectly.

The other reason is that I recently ran across my copy of the Penycuik Experiments by Professor James Ewart. The Penycuik Experiments were conducted in the late nineteenth century. I originally found the book when looking for information on the Highland Ponies of Rhum, which are interesting because they are associated with the silver gene as well as the “tiger eye” trait. The text proved to be a dead-end for that, but the experiments described were really cool. I thought it might be fun to share them here, in part because the hybrids are interesting and in part because the experiment itself is a wonderful illustration of just how far we have come in our understanding of genetics in the last 100 years.

Professor Ewart was interested in disproving the theory of telegony, which was the belief that offspring from a cross could be influenced by the traits of the mother’s previous mates. While this might seem quite silly now, at the time the idea was almost universally accepted. Darwin mentions it in The Variation of Animals and Plants under Domestication, citing a case where a mare was crossed on a quagga and later produced horses with striping. The Penycuik Experiment was an attempt to recreate that situation to see if the theory of telegony held. The experiments are particularly interesting in that they predate the re-discovery of Mendel’s work by a few years.

The last quagga died in captivity in 1883, so Ewart used a Burchell Zebra stallion, Matopo. He crossed the Matopo, who is pictured at the top of the post, with a wide variety of mares. Among the first of the hybrid foals was Romulus, from the black Highland mare, Mulatto.

Most of the other hybrids looked much like Romulus – reddish brown ground color with an overlay of black stripes. Ewart also includes photos of the zebra hybrid bred by Lady Meux. In that case a Burchell’s zebra mare was crossed with a “Highland or Shetland Pony” with wall eyes.

He was said to be “light bay”, but in the photos above he looks chestnut. Unlike the other hybrid foals, his daughter does not have particularly visible striping.

She also looks like she might be chestnut, though it is hard to tell from an old black and white photograph. Another zebra hybrid, Birgus, was said to have grown up to be chestnut with black stripes. He was by Matopo and out of a chestnut polo pony mare. Photos of modern zorses suggest that in addition to black striping, the chestnuts also have black lower legs much like a wild bay.

What is interesting is that none of the hybrids in the Penycuik study had white markings of any kind. In addition to the wall-eyed pony stallion, one of the mares used by Ewart was a Clydesdale mare. White patterns can trump the zebra striping, which many have seen with the well-known tobiano zorse Eclypse.

The interesting thing about Romulus, and indeed all the other zebra hybrids, is that they had more stripes than their zebra parent. Ewart counted 43 stripes on Romulus, compared to the five between the shoulder stripe and hindquarter for Matopo. That seems counter-intuitive, that crossing an unstriped animal with a striped one might give the resulting offspring more stripes. That brings me to the other tangent I mentioned earlier. Tomorrow I’ll post about embryonic development and spot frequency, because that’s more really cool stuff.

Today’s Google Doodle celebrates the 189th birthday of Gregor Johann Mendel, the Augustinian friar credited with founding the science of genetics. (The link provided will take you to a really well-done interactive document that was part of an exhibit on Mendel at the Field Museum in Chicago.)

In honor of the day, it seems a good time to explain one of the basic concepts in genetics. I had a few people ask me privately about the wild bay variation, so I thought it might be helpful to include the explanation here where I can use pictures.

Often when I talk about coat color genetics, I use the image of a light switch. That is because one of the most common stumbling blocks to understanding is the idea that unrelated colors have dominant or recessive relationships. This misconception is clear when one hears things like “grey is dominant to black”. In fact, those two colors are controlled by separate, unrelated genes. Dominance is about how genes relate to their opposite, so instead of grey being dominant to black, grey is dominant to not-grey.

The light switch is useful, because viewed this way gene pairs can represent “on” and “off”. Is the horse grey? (Is the switch on?) Is the horse not grey? (Is the switch off?) The image makes it easier to understand how genes relate to one another.

This works because many genes are like grey, and only come in two versions: “yes, it is there” and “no, it is not there”. The analogy falls short, though, when talking about the genes that have more than those two options. The proper term for a different version of the same gene is allele. Genes with multiple alleles need a different approach.

For those genes, it is perhaps better to image the gene as an ice cream cone.

I have an ice cream cone (locus) and two scoops (genes) – one serving from each parent. For the moment, my options are vanilla with chocolate chips (the “on” from my switch analogy) or plain vanilla (no chips, or “off”). This gives me three possibilities – two vanillas, two chips, or one of each. This goes back to the classic 3:1 ratio discovered by Mendel, and familiar to most high school students taught to use a  Punnett Square. This could easily illustrate the situation with a simple dominant gene like grey.

Now we’ll make it more interesting by added a new option.

Here we have mint chip ice cream. It is still ice cream – it still belongs on a cone (the locus) – but it is a slightly different flavor. And I still have the option of no chips (off) or chips (on). It is simply a variation, an additional allele, of what I already had.

This makes things more complicated because I can mix and match any of the options. I can have no chips, mint chip or chocolate chips in any combination. The only limit is that I still only have room for two scoops. I have more options, but I still just have two parents, each giving me one serving. So I can have two scoops of mint chip, but if I do there is no room for a serving of chocolate chips.

From a genetic standpoint this is an important distinction because in most cases the genes, and therefor the colors, are completely separate. That means a horse can inherit colors without shutting out the possibility of others. When colors are variations of the same gene – when they are alleles – they actually do shut out possibilities, because there are numerous possibilities and only room for two genes. It also makes dominance more complicated, because not only will “on” or “off”  be dominant, but one of the two alternate versions will have to be dominant over the other.

Going back to the color that started the discussion, wild bay is one of four options at agouti. (That means for our ice cream scenario to work like bay, we’d actually need a third flavor of chips!) With bay the other options are regular bay, seal brown (sometimes called black and tan) and black. Because agouti (bay) regulates the production of black pigment, black can be thought of as the “not bay” option because the black is obviously not being regulated. The other agouti options are all dominant to not-bay (black). Wild bay is presumed to be dominant to regular bay, which is itself dominant to seal brown. That follows the general rule for mammals that colors that allow more expression of red pigment are dominant to those that allow less. The important thing to remember is that all four options are at the same place (on the same ice cream cone),  so a horse can only have two. They can have any combination, but still just two servings.