Genetics are confusing !

Even with their pedigrees in hand, the genetics my babies carry confuse me.

I *think* we basically worked out what our Mini Rex buck has - at least in part, but for our doe - the colour genotype calculate doesn't include Tri-Colours and Harliquins, leaving me baffled !

Can someone with more knowledge take a look at what Bug4H and I came up with via plenty of Punnett Squares and a few websites ?

For our buck :




And for our doe - this one has me confuddled !

You can go to
http://www.ephiny.net/tim/pedigrees/color_calc.php
and play with the various combos. You can even leave ones blank (like the other C or the E's).
Although there isn't a broken chocolate on the drop down, you can select chocolate, that will auto-populate most entries and then you can change the en, en to En, en

That's the main one I've been using, KenoshaRabbits - but I cannot figure out how to input Tri-Colours or Harliquins on it.

Between that, and the squares, we got the buck somewhat figured out.
The Black Otter threw us for a bit, but we got it - at least I think we did.

Tri Color is on the E-extension; ej is it's notation. I believe it should be recessive to the normal extension.
A tri color is a broken version of a harlequin. So it also has the ej but has en,en (solid) instead of En,en (broken) or En,En (Charlie)

__________ Mon Jun 06, 2016 3:30 pm __________

Also Otters have the at gene at the A site. It's phenotype would be at,_

Harlequin:
?? B_ C_ D_ ej_ enen

Tri-Colour Black
?? B_ C_ D_ ej_ Enen

Red:
A_ ?? C_ D_ ee enen

Does that help? I'm happy to give more detail but I thought it would help you more to try to work through from there yourself...

Also, why do you have so many ?? at the E locus? The visually self offspring from E_ x E_ is always E_. Plus I think most people would assume any visual self is E_ unless there was a specific reason to think Es was a possibility (on the other hand I'm not sure they'd be right to do so). If you are assuming Es is around, how have you identified the E_?

EDIT: Fixed an error. Only the visually self offspring from E_ x E_ are always E_. This is because the only other possibilities are ej_ and ee, neither of which can make a self.

twr":3gzqhy7i said:

Also, why do you have so many ?? at the E locus?

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I left blank anything we couldn't immediately and easliy identify.

Since both the buck and doe are broken chocolate they will be E- at the extension locus. ej is recessive to E.

twr":ym3tpoya said:

Also, why do you have so many ?? at the E locus? The offspring from E_ x E_ is always E_. Plus I think most people would assume any visual self is E_ unless there was a specific reason to think Es was a possibility (on the other hand I'm not sure they'd be right to do so). If you are assuming Es is around, how have you identified the E_?

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E_ x E_ will produce E/E, E/(Es, ej ,or e)buck, E/(Es, ej ,or e)doe or (Es, ej ,or e)buck/(Es, ej ,or e)doe.
It's probably best to leave anything blank you are unsure of.

We are trying to determine what colours we could possibly get if we bred the two.

Could the tri-colour, harli, or red show up ?

alforddm":1lkpkpv9 said:

Since both the buck and doe are broken chocolate they will be E- at the extension locus. ej is recessive to E.

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Sorry that is incorrect. The broken gene is different from the extension gene. Unfortunately both extension and broken use "e" in their notation.

__________ Mon Jun 06, 2016 4:02 pm __________

HOWsMom":1lkpkpv9 said:

We are trying to determine what colours we could possibly get if we bred the two.

Could the tri-colour, harli, or red show up ?

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You could end up with a tri-colour or a harlequin.
I don't think you can get a red. I believe a red needs Agouti - A. Your rabbits have aa - full.

As for what you'll get that's a mystery until you get the full genotype for your rabbits. And catch-22 you can't get the genotype without breeding. <br /><br /> __________ Mon Jun 06, 2016 4:36 pm __________ <br /><br /> Actually, I did a quick refresher on color genetics. I would say it is possible yet unlikely you will get a tri-colour or a harlequin.
Both your buck and doe should have a E_ phenotype. There is a possibility your doe has the recessive ej. The only way to get a tri or harlequin is if you buck has a recessive ej or the recessive e.

If you are still in contact with the people you bought the buck from. Ask if there were any torts or tri/harlequens in that line? The breeder might not have records of the other litter mates, or can't remember, or it could be a recessive that has always been dominated. So a no answer isn't the end of the world.

KenoshaRabbits":1ri0cd4n said:

alforddm wrote:
Since both the buck and doe are broken chocolate they will be E- at the extension locus. ej is recessive to E.

Sorry that is incorrect. The broken gene is different from the extension gene. Unfortunately both extension and broken use "e" in their notation.

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I was referring to the chocolate part of the equation not the broken. Since they are both chocolate they must both be E- at the extension locus (MCR1). Broken (en) is on KIT.

KenoshaRabbits":1ri0cd4n said:

You could end up with a tri-colour or a harlequin.
I don't think you can get a red. I believe a red needs Agouti - A. Your rabbits have aa - full.

As for what you'll get that's a mystery until you get the full genotype for your rabbits. And catch-22 you can't get the genotype without breeding.

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They could end up with a chocolate tort (with or without broken) or a chocolate torted harlequin . The doe will carry either ej or e depending on her sires genotype. (Tri's can only be ejej or eje) The buck we can't be sure about. If you breed them and get chocolate torts or chocolate torted harlequin's then you will know.

alforddm":2ko4eolg said:

I was referring to the chocolate part of the equation not the broken. Since they are both chocolate they must both be E- at the extension locus (MCR1). Broken (en) is on KIT.

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My mistake I did think you where referring to the broken aspect of the parents and not the fact the fact they were chocolates.

I my last post I finally realized after a refresher on the E that they should both be E_ as you pointed out.

twr":236du28n said:

The visually self offspring from E_ x E_ is always E_.

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KenoshaRabbits":236du28n said:

E_ x E_ will produce E/E, E/(Es, ej ,or e)buck, E/(Es, ej ,or e)doe or (Es, ej ,or e)buck/(Es, ej ,or e)doe.

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I would interpret E_ as ruling out Es (if Es were possible but not certain I would expect to see either ?? or perhaps ?E). Under this interpretation, my statement is correct. But perhaps this interpretation is strange? I don't understand why you mention buck and doe (in particular, the "x" in "E_ x E_" indicates "crossed with" not an X-chromosome).

HOWsMom ":236du28n said:

Could the tri-colour, harli, or red show up ?

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Your doe certainly carries either ej or e (but not both). So if the buck carries ej or e you could get either tri-colour and harlequin or tort and broken tort (but you wont be able to get both harlequin and tort). The information in the pedigree suggests that the buck is unlikely to carry ej or e but pedigrees omit information about litter mates, which can be critical. If the buck had a single tort sibling then the probability he carries e is 66%, despite the pedigree. Even a tort half-sib would indicate a 50% chance he carries e.

Lilac is fairly likely just from the pedigree. I make it a 22% chance that both parents carry Dd, making lilac possible. If lilac is possible, 25% chance per kit.

twr":1epqawpq said:

twr":1epqawpq said:

The visually self offspring from E_ x E_ is always E_.

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KenoshaRabbits":1epqawpq said:

E_ x E_ will produce E/E, E/(Es, ej ,or e)buck, E/(Es, ej ,or e)doe or (Es, ej ,or e)buck/(Es, ej ,or e)doe.

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I would interpret E_ as ruling out Es (if Es were possible but not certain I would expect to see either ?? or perhaps ?E). Under this interpretation, my statement is correct. But perhaps this interpretation is strange? I don't understand why you mention buck and doe (in particular, the "x" in "E_ x E_" indicates "crossed with" not an X-chromosome).

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First I can clarify what i meant. An E_ crossed (x) with E_ will produce one of four possibilities, an EE, an E with the buck's recessive, an E with the doe's recessive or the combo of the parent's recessive (this assumes the unknowns are recessive). So for example Eej crossed with Eej will only result in Eej 1/2 of the time. 1/4 will be EE and another 1/4 will be ej/ej.
Now when you get the litter you can't tell the Eej's from the EE and further experiments would be needed.

__________ Mon Jun 06, 2016 7:06 pm __________

Also I believe E is dominant over Es.

As OP said, genetics are confusing

__________ Mon Jun 06, 2016 8:12 pm __________

twr":1epqawpq said:

HOWsMom ":1epqawpq said:

Could the tri-colour, harli, or red show up ?

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Your doe certainly carries either ej or e (but not both). So if the buck carries ej or e you could get either tri-colour and harlequin or tort and broken tort (but you wont be able to get both harlequin and tort). The information in the pedigree suggests that the buck is unlikely to carry ej or e but pedigrees omit information about litter mates, which can be critical. If the buck had a single tort sibling then the probability he carries e is 66%, despite the pedigree. Even a tort half-sib would indicate a 50% chance he carries e.

Lilac is fairly likely just from the pedigree. I make it a 22% chance that both parents carry Dd, making lilac possible. If lilac is possible, 25% chance per kit.

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You are correct up until the lilac percentages. The buck has a 2/3 chance of being Dd. The doe is unknown since the Tri-color chocolate is full of unknowns. Without known genotypes you can't get an accurate probability.

However, is one assumed the best case scenario of both the tri color's parents being Dd the best case scenario is the doe has a 1/2 chance of being Dd and a 1/3 chance of both parents being Dd.
Worst case the tri color's parents are both DD; the doe has a 1/6 chance of being Dd, and a 1/9 chance that both are Dd.
If one of the tri colors is Dd and the other DD; the doe has a 2/9 chance of Dd, and a 4/27 chance both are Dd.

E is DEFINITELY not visually dominant over Es, or even fully visually dominant over ej.

E_ only rules out Es in cleanly viable genotypes that exclude Es, such as chestnut(opal, lynx, etc) chinchilla, or red or tort. (There are a few more.)

aa self can hide Es_ completely, or, the Es_ gene can completely hide an agouti as a self.

It's just plain impossible to tell them apart visually, and test breeding requires sourcing animals who have been confirmed to have unusually clean genotypes, since AA EE gives the most reliable results...

The Es gene can turn a whole line upside-down genetically. :lol: For example, a rabbit that looks like it should be
aa B_ C_D_ E_
Can easily be
A_ B_C_D_ Es(Es, ej, or e) and I strongly believe EsE too.


I say easily,
because almost every third genetic question post on facebook seems to be from people wanting to know why breeding two visual selfs together is producing visual agouti or steel.
(Yes, I've even seen some stunning steel rex recently.)


I've actually started to believe that a_ might be a rare genotype in the US. :lol:

I'm somewhat more confused now. *sigh*

Okay so.

For Mischief's sire Shotgun, he is AabbC_D(d?)eje(I was told he carries dilute)
For Mischief's dam, Para, she is aabbC_DdE_(was told she carries dilute, because was told they produced lilac when bred together)

Mischief is either aabbC_D_Eej or aabbC_D_Ee, can't be sure til she produces.

Chaos, on the other hand, is most likely aabbC_D_EE, just based on his pedigree, but again, won't know til they breed.

My best guesses for offspring are going to be solid chocolate, broken chocolate, charlie chocolate, with a possibility of solid, broken and charlie lilac as well.

There is a chance that Chaos could be Ee, which would open the possibility of solid, broken and charlie chocolate harlequin(broken would be choc tri, like Shotgun) or solid, broken and charlie lilac harlequin(broken would be lilac tri) IF Mischief is Eej.

If Mischief and Chaos are both Ee, you would also have the possibility of solid, broken and charlie chocolate tort(non showable colour) or solid, broken and charlie lilac tort(also non showable colour).

Mischief had an amber charlie and solid chocolate in her litter. Chaos had umpteen million broken and solid chocolates in his litter(there was 7 all told).

Thank you.

As confusing as it all is, it's kind of fun to try to put it all together.

Bug4H":2m6juhyw said:

I'm somewhat more confused now. *sigh*

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I feel I should apologise for overcomplicating things, particularly when I unnecessarily brought up probabilities. I should have known that that wouldn't help.

twr":1ig6yn1z said:

Bug4H":1ig6yn1z said:

I'm somewhat more confused now. *sigh*

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I feel I should apologise for overcomplicating things, particularly when I unnecessarily brought up probabilities. I should have known that that wouldn't help.

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Me too, sorry it is not often that my math nerdiness and my rabit nerdiness come together.