Tag Archives | alleles

A family of diverse colors

SabTobHalf

It was perhaps a bit rotten of me to bring up the tobianos and dark-headed roans when talking about the confusion about what to call horses with sabino patterns. Instead of saying, “No, this really is pretty simple,” I opted to point out that it is even more complicated. Now that I am feeling a little less mischievous, I probably should attempt to clarify things a bit.

I began this (meandering) train of thought with a post about the change from Mendelian genetics to molecular genetics. That is, a shift from analyzing colors using visual identification and statistical analysis to understanding colors based on the changes to the genetic code. Using the first method, colors were grouped a certain way that has become familiar to many horsemen. When the colors are grouped according to the gene where the mutation occurs, however, they sort a little differently than expected. Colors that look quite different – colors that aren’t even thought of as belonging to the same basic category of modification, like tobiano and dark-headed roan – can be mutations to the same gene.

The technical term for this situation is allelic heterogeneity. In plain English, what that means is that there are a number of different options for one gene. In the case of these particular colors and patterns, the gene where they are found is called KIT.  Tobiano, roan, sabino and dominant white are all alleles at KIT. As different as they look from one another, they can be thought of as belonging to the same family. This may seem a bit esoteric, but it has a couple of implications for breeders.

The Spotted Saddle Horses pictured at the top of this post display a type of tovero pattern that is very common in their breed. The ragged, torn outline of their spots is typical of what happens when tobiano is paired with Sabino1. It is a compound heterozygous pattern. That is, both copies of the KIT gene have a mutation, but they are different alleles. If that same horse had two copies of tobiano (two of the same allele), we would call him a homozygous tobiano. Instead these horses have one tobiano and one Sabino1 (two different alleles for the same gene). A horse has two copies of a given gene, but they only get to give one of them to each of their offspring. So like the homozygous tobiano, if they were bred to a solid horse all their offspring will be pintos, but only half will be tobiano. The other half will be sabino.

Sb1HeteroHalf
Bred to solid mates, half the offspring of the toveros above should have this kind of pattern – Sabino1.

Allelic relationships like this are important to breeders because it means that under most circumstances, the patterns that result from combinations of alleles are not going to breed true. That might not be important if all that matters is that the resulting foal have a pinto pattern, because a compound heterozygote is going to produce a patterned foal 100% of the time. But if a breeder wants to duplicate the original combination, that might matter quite a lot. And if the other “pattern” is something that would not qualify as a pinto, like dark-headed roan or one of the more minimal versions of sabino, then the 50/50 nature of the inheritance might be a problem.

Breeders have noticed that some combinations, like tobiano roan, are difficult to get consistently. That is because this same splitting of the two alleles occurs; the horse can only give one but not both, so the only way to repeat the combination is for the other parent to contribute the second allele. The fact that some of these alleles look so different from one another makes the relationship between the colors less obvious. Knowing why Sabino1 toveros do not produce their own color when bred to a solid mate allows breeders to pick crosses that stack the deck in their favor. (A cross to the same Sabino1-tobiano combination, for instance, would give the desired pattern 50% of the time.)

The connection between these seemingly different colors might also make it easier to understand some of the quirks within some of these patterns. One of the most common questions I get from breeders of tobianos is about roan patches, or roaning in the colored areas of the coat. It is a relatively common occurrence in tobianos, and it often causes breeders to inquire if their horse might carry some kind of sabino pattern. In many cases, it appears that the roaning is just part of the tobiano pattern itself.

Dexter2
Dexter has diffused roaning throughout the dark areas of his coat, with somewhat greater concentrations of white hairs around the borders of his spots

RoanPatch2
Here the roaning is mostly limited to one patch, though colored specks remain inside the roaned area

When tobiano is understood to be a mutation to the same site as both roan and sabino, irregularities like these seem less surprising than when tobiano is thought of as something wholly separate. Likewise, the idea that tobianos might be more prone to white on the face than solid horses seems less outrageous. Tobiano is related to a whole group of patterns that can quite rightly be described as doing just that, after all! (For newer readers, more on my scandalous views on tobiano face white can be read here and here.)

In fact, knowing that these colors are alleles of the same gene is useful because it encourages us to think about them in a different way. If we know that KIT mutates frequently, giving a surprising number of white and sabino variations, what about roan? Roan has proven problematic when it comes to testing, which suggests there is more than one version of the color. It is also true that there are quite a few instances of spontaneous “roans” in a variety of breeds. These have been dismissed in the past as not “true roan” because they came from non-roan parents. But what if they are just one of many roan mutations? And what about the various forms of white ticking, like rabicano and salpicada? Are they roan variants on KIT, too? Given what is known about the white mutations, that seems like a reasonable theory.

Taken as a group, many of these colors and patterns blend together with a lot of overlapping traits. Which brings me back to the original question, which is what to call them all. I’ve skipped over the more pressing problem of sabinos and dominant whites in this post, but I wanted to highlight the connection between these different colors and introduce the idea of compound heterozygosity. It is an idea that is pretty important to the situation with the sabinos. I had hoped to wrap this subject up with just one more post, and start posting some less in-depth topics, but it is probably obvious why I have avoided posting about this before. It is not a subject that lends itself well to brevity! So next up, the other group of KIT mutations and some ideas about what to call them. I promise, eventually I will get back to some easier topics!

KitComic

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Happy birthday, Gregor Mendel!

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 thought to be 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.

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