Rabbit 

Basic Coat Color Genetics

Please excuse our mess while we work on these sections!!!

Okay, for all the non-genetics folk out there, a little terminology 101. Genetics won't be quite as painful once you know some of the jargon. Think of it like starting new in the fancy. I'm fairly sure there were a lot of breed specific and species specific words you had to learn. Genetics is no different. So with that in mind, there are just a few words you need to know the definitions for. Once you've got those, the rest will seem easy. These are going to be my paraphrasing for you for ease of communicating. Feel free to jump in anytime with questions.

Genetics is the study of inheritance. That's about as basic as I can get with that one. Of course there's more to it, but that's generally it (as far as animal breeders are concerned).

a Trait is anything we select for based on an animal's appearance. Such as coat type, coat color, eye color, crown, shoulder width, etc.

Phenotype is how an animal looks to us on the outside. We show according to this.

Genotype is the animal's specific lineup of genes on the inside.

a Gene is the mode of inheritance. Merriam-Webster dictionary has this really long definition of a gene, which includes several much longer words that I refuse to utter here. Most of you probably know what a gene is without having to put it into words. Examples would be coat length, mature weight, black coat color. They are quite specific.

In simple inheritance, one gene controls one trait. Most of the things we select for in rabbits, are simply inherited.

In complex inheritance, one trait is controlled by many genes. Most of these we are not consciously aware of, as they are difficult to trace. Most of the type traits are complex inherited. Progress is slow as a consequence of the many genes involved.

a Locus is the place where a gene is known (or believed) to exist. (plural is loci)

an Allele is each "type" or alternative form of a gene that can occur at a single locus. So if the gene is the black gene, there would be 2 alleles, B for black, and b for chocolate. There are some genes that have more than 2 possible alleles, such as the color locus, where you can have C, full-color; chd, dark chinchilla; chl, light chinchilla; ch, himalayan; or c, albino. Only 2 alleles can be present at any single locus. So even though there are 5 possible alleles for the color locus, only 2 will be found in any one animal for a single gene.

Dominant is one allele that asserts it's effects over others. The Black (B ) allele is dominant to the brown (b ) allele. Agouti (A) is dominant to the tan (at) allele, and both are dominant to self (a).

Recessive is one or more alleles whose effects may be hidden by other alleles. Dilute (d) allele is recessive to the non-dilute (D) allele.

(these 2 are actually a little more complex than this, but I'm trying not to confuse)

Homozygous (also homozygosity and homozygote) is where both alleles at a locus are the same. A self is homozygous aa, a vienna is homozygous vv.

Heterozygous (also heterozygosity and heterozygote) is where the two alleles at any given locus are different. A broken is heterozygous ENen.

Complete Dominance is where both the homozygous dominant and the heterozygote exhibit the same phenotype. At the agouti locus, AA and Aa will both be agoutis, while only aa will be self. We say that agouti is completely dominant over self.

Incomplete Dominance is where the heterozygote acts as an intermediate between the two homozygotes. At the broken locus, broken is the intermediate between solid and charlie. We say then that the broken gene is incompletely dominant.

I think that pretty much covers the basics of the terminology. Next I'm going to mention a few specific genes of interest. 

All genetics uses a letter abbreviation to identify the alleles in a string of genes. Generally these are the first letter or the first two letters of the name of the dominant (or recessive) allele of the gene. Originally, the dominant allele was used, but over time it has switched somewhat to the recessive. Unfortunately, some genes were already being identified by the other form and thus didn't change. 

What does this mean for the average new genetics pupil? A whole lot of confusion! However, bear in mind that while rabbit folk might have adopted one or two identification letters for the genes, that doesn't mean that everyone everywhere uses the same. Fact is that in genetics, there really is no standardization. That means that sky's the limit as long as you explain what they stand for to people.  It also means that you should never correct someone that does it differently, just read on or ask what they are using the letters to stand for.

An example would be the dwarfing gene. Old-time gene identification means that the recessive (dwarf) allele would have been shown as d and the non-dwarf allele as D. In many circles that is no longer the case, with dw being shown as dwarf and Dw as non-dwarf. My point is that both are perfectly acceptable ways of showing the two alleles as far as geneticists are concerned. So don't sweat the letters too much. 

That being said, you probably should still have a general idea which letters are currently used in the genotyping of rabbits. (that way you can seem really impressive to others when you can write it down for them!!) I'll go into more depth soon, but these are the main color genes you'll be dealing with: A, B, C, D, E, EN, Du, W, V, Si, & P. Now let's get going on these.

There are 5 main genes in rabbit coat color genetics. All breeds have these 5 genes (some have others too). They are agouti, black, full-color, dilute, and non-extension. Let's look at the first gene in the series: agouti.

Everyone knows (or should know) what a basic agouti rabbit looks like. It's the wild type gene configuration. All dominant in all 5 of the main color genes. But the first gene locus is the main controller of the agouti coloration. It causes multiple colors or banding on each individual hair, giving the animal a mottled appearance, a brownish/reddish look.

There are 3 alleles associated with this gene. The agouti allele (A) is what causes the banding of the hairs. It is the most dominant of the 3 alleles and is responsible for any variety that consists of multiple colors including the 4 basic agouti patterns, the four chinchilla colors, tri's and harlequins and magpies, and steels. All of these have multiple colors in the coat, either on each individual hair (banding/tipping) or in color patches (tri/harly/magpie). When there is an agouti allele present, all other A locus alleles are hidden. It is completely dominant. So AA, Aat, & Aa will all be agoutis.

The second in the line of dominance is the tan allele (at). It restricts color on the belly and in the "liner" markings (neck triangle, belly demarcation, nostrils, ear edges, etc). This one is responsible for otters, martens, and foxes of all varieties. It is completely dominant over the remaining allele, self. So it only takes one of these alleles to have those coveted varieties.

The last (but certainly not least) allele found at this locus is the self allele (a). This one is the most recessive of the three and will always be masked in the presence of the other two. All banding is restricted over the entire body by this one. It takes two of these little guys to get any of the selfs since it is constantly overshadowed by it's two older brothers.  I'm sure many of you are familiar with the 4 main varieties of self, but these are also responsible for torts, shadeds, himalayans, & pointeds (sable point, etc).

Now for the really fun part. Since each parent can contribute only one allele to each offspring created, that means that you can use a little deductive reasoning to figure out who has what. Two selfs can contribute only an (a) allele each, so all the babies will always be self in the regard. That is the only certainty that we know. Two agoutis *can* produce self, tan, or agouti (but never all three! remember that at is dominant to a, so if you cross Aat X Aa, you will get AA, Aat, Aa, and ata which would be tan).

I read once in a rabbit genetics book, that all rabbits are really only two colors: black or brown. Once a genetics pupil can accept this basic certainty, the rest will fall into place. 

That's not exactly verbatim, but gets the idea across. And they're right. All rabbits you have ever seen and all rabbits you will ever see can only be either black or brown. As a result of this fundamental gene that I'll discuss here. Every rabbit that has ever existed has this gene in one of three forms (BB Bb bb). It's probably the simplest of all the genes, and the easiest one you'll ever have to grasp. Remember, black....brown. 

So what does that mean, exactly? It means that the black locus is very basic and always must be taken into account. It means that every other color variety is a variation of these two. There is no half-way for this gene either, it's all or nothing (completely dominant). There are only 2 alleles for this one. Care to take a guess what they are??  Yep, black and brown!

The dominant allele for this one is the black allele (B ). And it is complete, it hides the presence of the brown allele where applicable. I don't think I have to say much about the black allele. This one is the wild-type allele and is found in chestnut, chinchilla, black otter, black steels, black fox, black tort, black himi, sable point...the list goes on and on.

The recessive to this one is the brown allele (b ). This one is often referred to as the chocolate allele and is certainly acceptable to use in substitution.

Well let's continue. I'm still working on the post for the full-color allele (C ), but don't quite have it ready yet. It's a long one, but in the meanwhile, I'll skip to the next gene: dilute (D).

The dilute gene basically causes blues and lilacs. It results in a lessening of black and yellow pigmentation where applicable. Thus we say the gene causes dilution of the black/brown gene.

There are two alleles associated with this locus, dilute (D) and non-dilute (d). Simple, eh? This one is also completely dominant, being that a rabbit that has just one D allele will not demonstrate any dilution. Non-dilute varieties include all of the black and brown series varieties. (black, chocolate, chinchilla, choc chin, chestnut, choc agouti, etc.)

Just like the black/brown allele, you must have 2 dilute alleles (dd) to have an actual diluted rabbit in appearance. The diluted varieties are all of the blue and lilac series varieties. (blue, lilac, squirrel, lilac chin, opal, lynx, etc.)

The last two main color loci are somewhat complex due merely to the number of alleles that can be present causing different variations. But it is these wide variations that give us such a myriad of varieties that we so take for granted (especially in the breeds where so many are accepted for showing).  I will get to the color locus in the next post, but I want to cover the non-extension gene first.

Many of you are probably familiar with this gene, but might not fully realize it. This gene mainly acts on the agouti locus to cause variations in how that gene affects the coloration of the rabbit. It is also completely dominant with each allele overshadowing the effects of the alleles below it.

The most dominant allele of this gene is the steel allele (Es). Combined with an agouti allele at the A locus, you'll get the traditional steel rabbits with only the outermost band on each hair shaft (ticking). However, this gene combined with anything other than agouti at the A locus will not be able to show steel. Instead it will result in the gene not being visible, but may show itself as soon as the agouti pattern is returned to the genetic lineup.

The second in line of this gene is the full extension allele (E), which does exactly what it sounds. Or more basically, it does nothing at all. This is the traditional wild type allele found in most of the common color varieties. All 4 self colors, chestnut, opal, chocolate agouti, lynx (the true lynx only though), the otters, the martens, the himalayans, etc.

The third most dominant allele for this locus is the japanese extension (ej) allele. This one is most notable for causing harlequins and tri-colors. If you were to observe these colors, you can see how the ej allele acts on the agouti locus. It alters the mottling of each individual hair shaft into a pattern of mottling over the entire body. This allele is responsible for all of the harlequin and tri-color (broken harlequin) colors, but also all of the magpie colors.

Finally, the lowest of them all is the non-extension (e) allele. This one can be a fun allele to play with in your varying breeds.  It removes the B/B/C/L (black/blue/choc/lilac) color from the base and tip of the hair, leaving a yellow hair shaft and lightening the undercolor. It's not perfect though and can leave some "shadowing" this can most commonly be seen in the torts, which is a non-extension self. Other non-extension varieties include the red series (red/orange/fawn/cream) & the foxes (tort otters).

Okay, now for that last one and one of the most complicated of all the genes. The color gene! Now a lot of people are probably familiar with this gene, though may not be entirely aware. These are your "shaded" rabbits (remember torts don't count, they aren't really shaded). There are a whopping 5 alleles associated with this gene. Just remember, there can only ever be two residing within any rabbit you come across. And generally, they aren't too difficult to tell apart. smile.gif The dominance of this one is generally complete, with higher dominance alleles overshadowing the effect of each lower recessive allele.

The most dominant allele in this gene series is the full-color allele (C ), which essentially does exactly what it sounds like. The full range of pigmentation is expressed over the body. It will hide all the other alleles that might be present at this locus. Test breeding and ancestor examination may reveal the hidden allele, but not always. All of your basic non-shaded varieties have at least one of these alleles. So the 4 agoutis, torts, otters, foxes, most steels (some exceptions), basic tri's and harlequins.

The second and third alleles in this gene are tricky in their dominance. They are the dark chinchilla allele (chd) and light chinchilla allele (chl). For ease of communication, I'll call them by their familiar names: chinchilla (chd) and sable (chl). These both cause similar effects in the coloring of agoutis, with dark chinchilla resulting in a darker appearing animal (generally). Let's look at chinchilla first (chd).

Dark chinchilla, or chinchilla, is just as it sounds, it's causes darker shading and restricts yellow pigmentation (removes all but one and leaves black alone). So if you remove the yellow from the hairs of a chestnut agouti rabbit, they would appear to be silver from the alternate banding of black, white, and grey. Because no red would be able to be present. This means that all agouti rabbits with a chd allele would appear chinchilla. This is not affected by the other 3 color variations (chocolate, lilac, or blue) would still not be able to show yellow pigmentation. The best chinchillas have 2 of these alleles, with light chinchillas generally having one plus one of the lower alleles. These will be your 4 chinchilla varieties, self chins, martens, and magpies.

Light chinchilla, or sable, causes somewhat lighter, brownish shading over the body. It removes all yellow pigmentation and lightens the black to a more brownish coloration. One of these alleles in conjunction with a lower recessive will yield an animal with dark shading over the extremities and belly, and lighter coloration along the back, though not always. Single allele sables *can* have even dark chocolate shading over the entire body (known as a dark sable). Two of these alleles will yield seal, which is a much darker brown color than even the dark sables. Though seal may sometimes be confused with a black, the genetics will always reveal themselves with a breeding to any of the lower recessive colors of this gene (REW, cal/himi). These varieties include the sable/seal varieties, sable chin varieties, sable martens, and sable magpies.

Below the chinchilla alleles in the dominance scheme is the himalayan allele (ch). This gene causes the color of the rabbit to be temperature sensitive and as such restricts color to the points of the animal (nose, ears, tail, feet). In the presence of any of the higher alleles, it will not be exhibited. The best colored himi will have two of these alleles, though a rabbit with a himi and rew alleles wil still be himi. However, the color may not extend as far along the points as it would in it's homozygous form. These are (of course) your himalayan/californian rabbits of all breeds (in B/B/C/L), and also agouti himalayan (also known as "chin himi") You can also have a marten himi (has the tan gene), and (in theory at least) a magpie himi, though I've yet to actually have seen one. I'd probably be severely creeped out if I did. But as far as genetic theory is concerned, it should be possible. Genotype A- B- chc D- ej- 

Finally (I know you all are probably cheering to see the end of this one! lol) we have the lowest of all in this series, and probably one of the most fascinating in how it conducts itself. It is the albino allele (c ), which causes the complete absence of pigmentation to be seen on the animal. This includes hair, skin, and iris pigmentation. The result (as many of you are aware I'm sure) is a white animal. But the most interesting thing about this allele (and remember that you'll only ever see an albino rabbit with two of these) is the fact that it has the ability to hide *all* other genes found on the animal. So next time you see a "white" rabbit, I want you to picture a rabbit with a white towel thrown over it.  That is the equivalent to what you are seeing. The only way to know what is being hidden by the albino gene is to breed to something else. Whites are VERY useful if you are wanting to isolate out the hidden recessive on the color locus, since you will always get the two of whatever the *other* rabbit has on that locus.

Clear as mud yet?? 

Just remember something very important. Two rew rabbits can only contribute a (c ) allele to each of their offspring. So every single baby in a rew to rew breeding will be white. There is no doubt, no alternative, no recourse. If someone tells you they got something else, then their records are incorrect. I would also like to note that a white rabbit *can* produce a broken when bred to a solid colored rabbit. That simply means the white is a hidden broken (white broken by white is still white lol). If you get 100% brokens in every litter, then the white may be a hidden charlie. wink.gif

I'll pause here if anyone has any questions, then we'll start on some of the more obscure genes that not *everyone* will deal with on a regular basis.

Intermediate Coat Color Genetics

I thought this thread would be useful in helping people to "put it all together" because even though you can *know* all the genes of rabbit coat color genetics, the truth is that you'll never really be able to use it unless you understand that there is no rabbit out there with just a single color gene. The genes act and interact to give us our varieties. So while I may abbreviate an opal rabbit as A- dd, that doesn't mean it doesn't still have those other genes in there. The abbreviation simply hits the important genes to get the color across with as little notation as possible. Cause let's face it, it would be a real pain to have to look at long strings of genes and try to translate each of them into phenotypes. BTW, the opal I mentioned would be A- B- C- dd E- enen V- W- Du- etc.

Let's start with the basics and we'll hit a few at a time.  Now then, since I have gone through the 5 main color genes already (please refer to the Basic genetics thread for additional info), we can look at how they all interact with one another to cause the rainbow of colors that we all as breeders know and love (or love to hate in some instances where not all of them are accepted lol).

The agouti gene as you know causes banding. The second locus is the black/brown gene, then color gene, dilute gene, and extension gene. Let's look at what happens when you combine agouti with the recessives from each of the other genes. If I were to combine just the agouti gene (A-) with only a single other recessive, say brown (bb), I'd have a chocolate agouti (cinnamon). The brown alleles cause the black banding of the chestnut to be chocolate.

If I were to combine the agouti gene with a pair of recessive dilute alleles (dd), then I'd have an opal. Blue (diluted black) would replace the black banding on the hair shafts and fawn (dilute red) would replace those bands. By the same token, combining the agouti allele with both homozygous brown and homozygous dilute would yield a lilac agouti (lynx). Because the chocolate/red would have been diluted and that would replace the black/fawn bands.  Good so far?

Those are the easy interactions with agouti. It gets harder with the remaining alleles. Combine agouti with the full color allelesin homozygous form and nothing will be different. Start adding in homozygous recessives, and things get interesting. Agouti coupled with homozygous dark chinchilla (chd) will yield a chinchilla rabbit. Couple it with a heterozygous chinchilla (chd-) and you'll still have a chinchilla, just maybe not as darkly colored. Couple agouti with a single sable allele (chl-) and you'll have a sable chinchilla, two of these (chlchl) will give you a seal chinchilla. Seal chin and regular chin would probably be difficult to distinguish. Sable chin usually has a brown cast (and ruby glow to the eye!). Agouti coupled with homozygous himi or heterozygous himi/rew (chch or chc) will give a chinhillated himalayan, or chin himi. And it won't matter if you combine agouti with homozygous rew, cause it'll be an albino. 

Agouti with the final allele, extension will give some interesting varieties also. Agouti with full extension has no effect. Agouti with either homozygous japanese extension or heterozygous japanese/non extension (ejej or eje) will give rise to tri-colors and harlequins. You need the agouti allele to have multi-colors on the rabbit. Couple the agouti gene with homozygous non-extension and you get your reds/oranges/fawns. An additional modifier (not believed to be an actual gene) makes the decision as to which intensity of those three the color will be, they all have the same written genotype. (if you see a genotype written with O/R/F, those are to indicate the modifiers visible and should be taken into account, but not necessarily passed onto the next generation) I've left the 4th allele of this gene for last because it has special circumstances. It is the steel allele (Es). While it is dominant over all others, it is worthy to note that this gene has special effects in it's homozygous form that acts to suppress the banding of the agouti allele. So a rabbit that is A- EsEs will appear to be self colored. Additionally, a rabbit that is A- Esej or A- Ese will also appear to be self colored. Only the combination of A- EsE will show the tipping that is distinguishable to steels.

If you start to combine the "simple" alleles that cause black/blue/chocolate/lilac with these others, you give rise to a whole complex of agouti varieties that include Cream = A- dd ee (R/O/F), Lilac Pearl Agouti = A- bb chl- dd, lilac chinchilla A- bb chd- dd, and so many many more. 

I'm tired now, but I'll start on some of the others later. For fun, see how many different varieties you can come up with for the agouti gene by itself. Can you name them all? How many of them have you seen? (I KNOW right off that I have not ever even heard of this variety: A- bb chl- dd ee or A- bb chd- dd ee)