trying to understand genetics

Rabbits are the only things we've ever bred. We had some idea what to look for in a dairy goat or piglets, and the advice to breed the best and eat the rest seemed like something we could follow. Now I'm trying to understand the hidden variables--partly because we're doing close breeding and have read that can lead to problems as recessive genes surface and partly because I'm terminally curious.
So one of the things I've been told is that as you line breed or inbreed, your herd will become more uniform in appearance. So all our rabbits are descendants of just one buck and doe. We bred to a young buck (grandson of original buck). One of the does was his mother, one his sister but a year older. In each litter there was one kit that was light colored on the underside (agouti?) All kits from our previous 4 years were one color all over (some were silvered, some had gold-tipped steel, but they were the same all over) so it surprised me to see these 2 kits.
Color doesn't really matter to us, but it makes me wonder what our herd will look like if they ever come to all look alike and what other traits may appear that we hadn't seen before.

Agouti is actually dominant to self (solid color,) but steel makes things tricky.
Your steels are just genetically modified agoutis ( with the base hair color extended by various amounts.)
Steel is a very dominant gene, and it is on a separate locus from self or agouti. It requires just one copy to modify an agouti coat, but is completely invisible on a self coat.

Some of your solids are probably also masked steels, which is just a steel with the base color extended across the entire hair shaft, mimicing the look of a self, but genetically still agouti.

Hidden modifier genes control what extent of the hair shaft is affected by the steel gene. I've seen the whole range of masked agouti, almost-self, nice looking steel, and almost-agouti in littermates.

Your kit looks opal, which is blue agouti, it's a gorgeous color.
You can tell it doesn't have a steel gene modifying it's coat because of the pretty white belly, eye rings, and ears. I usually call those "agouti marks," and everyone seems to understand. :lol:

Chestnuts or opals (visual agoutis) are possible because some of your original animals either didn't carry steel at all, or were not carrying two copies of it. By doubling up that lack of steel, you have produced a few animals that do not carry a single copy of the gene, which is all it would take to make them look like steels instead of agouti patterned. Since agouti is dominant to self, if you continue breeding with them you would eventually have more agouti and steel than self colored animals.

It's the confusion between self and agouti, and the ability to mask agouti that makes steel genes so undesirable in silverfox rabbits, and other self breeds.

If you want them to look more solid colored you could start by culling all of the visual agouti and steel rabbits. The problem is, with steels sometimes posing as selfs, you could have masked agoutis carrying the agouti gene hidden through many generations, to surprise you at random later.

Steel can be a bit of a headache that I luckily never really ran into.

You can breed the same color for 20+ generations and still have other colors show up. I've seen it with rabbits that were selected against a color and the breeders gave me very long pedigrees (in tiny print to fit on the page so a pain to read). Over time you reduce the odds of those genes still being there to pass on but every offspring has a chance of still getting the hidden genes forever unless you've bred to something that can prove the recessives no longer exist in the line. If you select various colors on purpose you can also keep a line of rabbits that started with lots of different color genes producing lots of colors. It's just hard to balance a desire to keep a color with other traits and people tend to end up looking at one or the other. Trying to keep a color will cause you to end up keeping an animal that is inferior to it's siblings in other ways or breeding for other traits will slowly make some genes less likely to occur.

A very basic example is if you bred a chestnut and black and only liked all the black offspring. They cannot have chestnut because agouti is dominant and appears (typically) if it's there so if you don't keep a chestnut you can't have hidden agouti and just eliminated it from your rabbits. Except in the case of steel messing with things and then sometimes a black is not a black and it's one of the few cases agouti is not always apparent. Recessives are trickier since if you bred a black to a blue or chestnut to opal and only kept the blacks or chestnuts you can still have dilute for blue, opal, and other colors it impacts as a recessive in your line. That's where some genes can pop up a dozen generations later. A rabbit can be sort of partially blue and not show it. You can get rid of black by only keeping blue but you can't get rid of blue for certain by only keeping black without test breeding if dilute is hidden in each rabbit.

Genes for body type are far less obvious and more complicated than color genes. Understanding colors doesn't really help you a whole lot in that area. In a more vague way it works the same as only breeding certain colors so some color genes disappear but there are so many variables and modifiers. It's more like breeding for the intensity of the color. If you breed lots of really dark rabbits of some colors you will eventually create a line that produces all darker than most but it will slowly go that direction without a clear line between which rabbits have which modifiers to only produce the darker shade of offspring. We only have some names for groups of modifiers like rufus that make more red appear in chestnuts, reds, and some other colors and cannot tell you what exactly is in each rabbit.

Clear as mud, right?

:lol: <br /><br /> __________ Tue Apr 17, 2018 7:08 pm __________ <br /><br /> In short, you had that color all along, but you also had a gene that was hiding it to varying degrees.
Anytime you have a visual steel, you have agouti genes for sure.

Thanks, Zass and Akane, for explaining. I still don't really understand even the color genetics--agouti and steel are dominant, but I only see steel in a few of my rabbits and had never seen agouti until these 2 recent litters with the young buck. Feels sort of like the emperor's new clothes to me. And I sort of knew what Akane said about other traits being harder to track or observe than color.
As I said, for our purpose (meat) color doesn't really matter. It's not something we select for, just something I notice as we're checking new litters to make sure all kits are fed. But when I first joined RT I read lots of posts about buying the best rabbits you could afford when you start and I wondered if we should be bringing in a new buck that was bigger, meatier. (Our SF starter buck was underweight for the breed--just over 7 lb) But the replacement bucks have been bigger, and our does, though smaller than the NZWs we started with, have kits that grow out as fast as those of our first does.
I just keep trying to imagine the gene pool we have, all the rabbits we've had from just one buck and doe, but if there are 'hidden' colors that show up over time, perhaps there are other traits that will become evident if we keep breeding the ones that are closest to what we want. People warn about the dangers of inbreeding, of what could show up, but I wonder if good things could show up, not just problems.
Sorry--I don't seem to be articulating this idea very well, but I am intrigued by all the possibilities in such a seemingly simple thing as breeding meat mutts.

Absolutely yes, good traits can show up as genes are concentrated, just like the masked colors did.

I think the hard to understand part is where steel genes sometimes make an agouti look like a self (solid) colored rabbit, so you may have been breeding a lot more agoutis than you thought.

In order to get the visual agouti, it requires just one agouti gene (it only has to come from one parent) and no steel genes, because steel will always always "muck up" an agouti and turn it into steel. Remember, a steel is just an altered agouti, so every steel you have carries at least one agouti gene.

You made them viable by breeding an animal with no steel at all (maybe a true self) to an animal with one copy of the gene, or else breeding two animals that one had one copy each, creating that 25% chance of steel-free kits. :lol:

Steel is not as simple of dominant as most genes. As it's written on most sites if they have steel then it should show up as steel when they are agouti and not show up if they are self. That should make all black rabbits from steels genetically self colors that can't produce agouti but in reality that isn't what always happens. You might be able to find some traces of discoloration from the agouti gene on what seem like plain self rabbits if you know what to look for. It's not a good gene to throw in there when learning genetics because of it's inconsistency. I usually ignore the exceptions it causes exist unless someone is already dealing with it. I only introduced one gold tipped steel doe and never had any surprises in the few breeders I kept from her to make more meat mutts for awhile. Zass I think found every last black Silver Fox in the area was actually a "malfunctioned" steel. :lol:

In the area? I had separate lines from seperate breeders in pa, ohio, georgia, and shoot, I can't even remember the last one, it was a few states away in another direction.. :lol:

It is nearly impossible to tell masked steel from a self with steel genes however, unless you have some pretty specific test breeding rabbits.

I've stared at so many kits till my eyes hurt trying to tell if they were true selfs or masked steels, and I've determined while you can tell from faint markings sometimes, other times you just can't.
It wasn't worth the eye strain. :roll: After a while, they were just "all steels until proven otherwise." :lol:

In facebook groups, I learned the steel issue was more or less prevalent throughout silverfox rabbits, with only a few people who's stock seemed to be free of it. It didn't matter much for them, because bringing in new stock would be nearly impossible without introducing it.

The rabbits with steel were just as good as any others for meat, anyway, if not better. It's been rumored that steels grow well, and I can't deny that those lines were my best growers ever. :shrug:

A first time doe kindled our third litter for the year yesterday. So our young buck is 3 for 3 and we just sold the old buck yesterday. Still puzzled about various things. Beau, the buck we sold was visually blue 3/4 SF and 1/4 NZW. Breeding to him we got a couple whites in most litters. Cloud, the young buck, is 5/8 SF and 3/8 NZW, visually black. So today's litter of 6 (the doe is visually black) has 3 dilutes in it, but still no whites.
Zass mentioned that there is some belief that steels grow faster and it is true that Casco, our best doe so far, is gold-tipped steel. But if all or most of the rabbits that look self are really steel, then how could one even begin to know if that was true about faster growth. I've observed, from my limited experience, that the whites don't grow out as fast. So far no white has survived the cut and been kept for breeding.
I hope now we can stick with this buck for a while. We really liked Beau but made the change when we had a promising young buck that had more NZ. But now we have 3 does that are his full siblings. The one that hasn't kindled yet was bred to Beau so we may want to keep a doe from her if she is a good mother and if there is a doe in the litter that seems promising. If we see no problems in the 2 litters from sibling breedings as they grow out, then we'll keep breeding them, I guess.
Anyway here are photos of the agouti from Garland's litter and the litter Hollis kindled yesterday.

I wrote this a while back and it might help. Once you get these combinations, adding the modifiers, dilutions, and white patterns is fairly simple.
http://colorgenetics.info/leporine-rabb ... k-together

For example, if you have a chestnut and add dilute you get opal, add chocolate and you get chocolate agouti, add them both and get lynx.
With a black rabbit, add dilute and you get blue, add chocolate and you chocolate, add them both and get lilac.

It takes different genes to get a dilute than a white. Although both the genes for dilute and for white are recessives and you'll need two of them before you see either blue or white.

In order to get white or blue, both parents must contribute a recessive 'c' (for the albino) or a recessive 'd' for the dilute. If one parent has it but the other one doesn't, then you won't see those colors in a litter between those two parents.

The blue buck that you sold had two recessive 'd's ( dd ) in order to be blue. The black doe he was bred with would have to have the color genes of aa B_ C_ Dd E_ if there were any blues in the litter. The blue buck would be aa B_ C_ dd E_. The blanks are because we see the dominant color expressed by the capitol letter and don't know if there's a recessive hiding behind it. A black rabbit has to be a solid color, so it's color code will start out with an 'aa'. Then, because it's black which is the dominant color, it must have one 'B'. However, there's two B genes in that location, since we see the black from the dominant B, we don't know if it is two dominant genes 'BB' or if it is one dominant gene 'B' with a recessive 'b' hiding behind it. Since we see black, it's gotta be either 'BB' or 'Bb'. But since we can't tell by looking at the rabbit, we just write it as 'B_'. If the black rabbit were bred to a chocolate rabbit with a color code of 'bb', then if there were chocolate babies, we'd then know the black rabbit has a 'Bb' and not a 'BB'.

In your newest litter, it looks like there's three blacks, a blue and several torts? The torts don't seem brown enough to be chocolates, but maybe chocolates?