New Zealand rabbit color genetics.

there are only 4 colors and their broken types of New Zealands. Black, Red, Blue, REW (ruby eyed white, albino)
These are the only showable colors of NZ's. Breeding them together can result in several colors that aren't showable (Tort, Fawn, Chestnut, Copper, Steel, etc, etc . . .) even in purebreds with long pedigrees. Yes, people do outcrosses for a variety of reasons, so even pedigreed rabbits may be carrying genes that one wouldn't expect to find in the NZ, but the presence of something other than a showable color in a litter doesn't automatically mean that the parents aren't purebreds.

cinnamon which has a brown base color

I have no idea what this is supposed to mean; "brown" has no meaning when it comes to either the genotype or phenotype of rabbit coat color (kind of like "gray" - there are scads of combinations of genes that can result in something that falls within the broad range of shades on the color wheel that could be called by that name). The color Cinnamon is a Chocolate Chestnut (Agouti), but a rabbit of the Cinnamon breed is a color called Tort, Tortoise or Tortoiseshell.
 
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When I look at this rabbit, I see a black rabbit with sunfading/staining on her coat. The brown doesn't appear to be a separate area of pigmentation within the hair shaft, it looks like areas where pigment that was in the hair has been degraded by exposure.

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When I look past the patches of obviously faded hair, I do see some that seem to have ticking. That looks like Steel. To get the "classic" Steel coloration, you have to have the Steel gene (Es) paired with the normal extension gene (E). Steel paired with either non-extension (e) or harlequin (ej) can appear solid black, or the rabbit may have varying amounts of ticking in the coat.

Though it may look like it in the NZ, Red is not a "self" color; it is an Agouti color with non-extension, wide-band, and rufous modifiers. If your doe has had offspring of non-extension colors, then yes, she must have a copy of the non-extension gene. She may also have a fair number of the rufous modifiers too, since the ticking in her coat appears to be a good bit darker than one sees in the typical "gold-tipped Steel."
 
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@jkeys0218 I skimmed through the blog post in your link, and I can see why you'd find it a bit confusing - the blogger is a bit confused themselves. In just the few minutes that I spent reading it, I found several mistakes, and even something that had me wondering what it was that they were trying to say. That's the problem with blogs; the poster may know what they mean to say, but they usually don't have a proofreader/editor to help them make it clear to anyone who isn't inside their head and thinking their exact thoughts.:rolleyes: For the most part, what they say is correct, but I particularly found their use of the terminology a bit, um, irregular. Looking past the rather jumbled jargon, they did hit most of the points right, so as a basic understanding of NZ genetics it does a decent job.
 
@Bunnylady How do the rufous modifiers work as far as passing them on? I know they work with different alleles to change the color, so are they not an allele? Dominate or recessive?
Do you have any recommendations for other reading material about NZ genetics?
 
That's a perfect example of what I mean by rather irregular use of terminology. Allele means one of the two or more forms that a particular gene comes in. The B gene has two alleles (B and b), The A gene has 3 alleles (A, At, and a), the C gene has 5 or more alleles (C, cchd, cchl, ch, and c; possibly cchm), etc. A rabbit has two copies of every gene (one inherited from its mother, and one from its father); they may be the same allele, or two different ones.

The only thing rufous modifiers do is change the amount of pheomelanin (the red/yellow pigment) that a rabbit can manufacture. You know how the bottle of yellow food coloring looks red? That's because the dye inside is concentrated. You put enough pheomelanin in a hair, and it begins to look red, too. Normally, there is just a little bit of yellow pigment in a rabbit's hair. Strip off the black pigment, and the rabbit's coat color would be somewhere between yellow and orange. The rufous modifiers just say "make more red." They don't change the amount of black, nor do they affect where in the coat the pigment appears.

There appear to be several rufous modifiers; some sources say 4, others think there are more. They are usually indicated as + or -; the more you have in the + form, the redder the rabbit will be. That's how polygenes work; each one doesn't have a lot of influence by itself, but they have a cumulative effect.

The inheritance of the rufous modifiers doesn't seem to be as simple as dominant or recessive. As I said, the more +'s you have, the redder the rabbit is, but if you breed a deep red rabbit with lots of rufous to one that is just a so-so yellow/orange, the resulting offspring will most likely be a shade somewhere in between that of the two parents, rather than one or the other. If + was dominant to -, or vice versa, you'd expect all of the babies from that cross to be the same shade as the parent with the dominant shade, rather than an intermediate shade. Did that make sense?

A good example of the difference rufous makes is the Rex color Castor. As far as the major color genes go, Castor is the same as Chestnut in any other breed (A_B_C_D_E_), but with the rufous modifiers ramping up the red pigment, it is a deeper, richer shade; more of a mahogany brown than a typical Chestnut. If you look closely at a Castor, everything else about it is just like a Chestnut; the only real difference is that the intermediate band on the body hairs is a sort of rusty red color, rather than the yellowish/tannish shade of the typical Chestnut.
 
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