Mystery harlequin - please help! Puzzled!

[sryglet]

Hello! I joined the forum because I breed harlequins and got a baby in a litter last year that makes absolutely no sense concerning my knowledge of rabbit genetics. We know the parent's lineage is correct on her pedigree and the color she is makes absolutely no sense!

Her dad is our black Japanese. Her mom is our lilac Japanese, born to our other lilac Japanese. She was back bred to her dad, meaning this baby's father and grandfather are the same rabbit. His parents were a lilac Japanese buck and a black japanese doe. Her mother's parents were black Japanese buck and a lilac Japanese doe. All rabbits in both parents pedigree are either black or lilac Japanese.

Her parents' pairing has produced 37 babies, all black, blue** (edited to correct) and lilac Japanese. Dad has produced over 200 babies and none had any white on them. Dad doesn't have any white on him. There is a zero percent chance that mom has ever been around another buck unless someone snuck a different buck into our rabbit run and he only managed to get one kit into a litter of 9 otherwise very obviously harlequin babies, and I'm pretty sure our dogs wouldn't let that happen on top of how weird that would be.

This baby was born pure white and developed small light and dark grey spots on her body, ears, and nose by weaning. Her grey spots have come in more and more over time - for instance, she did not have the smaller markings around her right eye until a few months ago and the markings around her nose have grown and darkened significantly over time. If that isn't perplexing enough, she has now begun developing pale fawn markings on her ears, nose, feet, and body at 6 months old (as you can see here), which are rapidly coming in now at 7 months. As you can see from some of the photos, she is beginning to develop darker fawn bands on her ears. Her ears were pale grey with absolutely no orange two months ago. I bathed her with whitening shampoo because I was certain it wasn't possible that these pale fawn markings were real, but they are definitely genuine coloration. I am absolutely perplexed about the presence of all three colors on her, as well as the fact that the spots appear and multiply over time. She's also smaller than any other kits we've produced and has a very masculine head shape.

Any clue as to what's going on? We sell show quality harlequins and I would be mortified if someone ended up with whatever this is in one of their litters from our stock - not that she isn't beautiful! We've sold a lot of babies and no one has ever reached out saying they got a random off-colored harlequin in their litters.

 

[Naelin]

Hello! I'm the person that told you to post here from Reddit.

I did some extra digging, and found someone that (purposefully) got a similar rabbit by crossing a harlequin with a broken sable colourpoint (Link and pictures here) A sable point would be aa__chl___ee, and the parts that matter here could perfectly have been hidden in your pure harlequins, and just take a lot of luck to get combined in the correct way to give this doe.

So the sire is black japanese and the doe is lilac japanese.
The mystery doe has for sure at least one harlequin gene, and seems to be blue (Are you REALLY sure that you got "all black and lilac" on the other 37 kits? Blue is much more probable than lilac with a black sire. They may be all black and blue.). This gives these genotypes:
Sire: <__B_C_Ddej_>
Dam: <__bbC_ddej_>
Mystery doe: <__B___ddej_>

As you can see, there is plenty of space in there for mystery genes on the parentss, especially for dad.
I am NOT an expert and I do NOT know exactly which colour this doe is, but I think she may have chinchilla light (also known as sable, <chl>) and one non-extension gene <e>, and on top she may be a self <aa>.
If both parents have a recessive gene on the C locus, and only one has non-ex on the E locus, that would give you only a 12.5% chance of a kit ending up with both things. If some other thing like aa is needed for this, the chance would be even smaller. Accounting for the luck of the draw it doesn't seem wild to me to see this for the first time after several pairings.

Still, it would be awesome if someone with more experience can give their opinion. @Alaska Satin sorry for summoning you but I'm very curious now, do you have a clue what may be happening here?

 

[sryglet]

Hello! I'm the person that told you to post here from Reddit.

I did some extra digging, and found someone that (purposefully) got a similar rabbit by crossing a harlequin with a broken sable colourpoint (Link and pictures here) A sable point would be aa__chl___ee, and the parts that matter here could perfectly have been hidden in your pure harlequins, and just take a lot of luck to get combined in the correct way to give this doe.

So the sire is black japanese and the doe is lilac japanese.
The mystery doe has for sure at least one harlequin gene, and seems to be blue (Are you REALLY sure that you got "all black and lilac" on the other 37 kits? Blue is much more probable than lilac with a black sire. They may be all black and blue.). This gives these genotypes:
Sire: <__B_C_Ddej_>
Dam: <__bbC_ddej_>
Mystery doe: <__B___ddej_>

As you can see, there is plenty of space in there for mystery genes on the parentss, especially for dad.
I am NOT an expert and I do NOT know exactly which colour this doe is, but I think she may have chinchilla light (also known as sable, <chl>) and one non-extension gene <e>, and on top she may be a self <aa>.
If both parents have a recessive gene on the C locus, and only one has non-ex on the E locus, that would give you only a 12.5% chance of a kit ending up with both things. If some other thing like aa is needed for this, the chance would be even smaller. Accounting for the luck of the draw it doesn't seem wild to me to see this for the first time after several pairings.

Still, it would be awesome if someone with more experience can give their opinion. @Alaska Satin sorry for summoning you but I'm very curious now, do you have a clue what may be happening here?

Oh my gosh, sorry I am on my phone rather than my computer and copied and pasted a lot of this from the original post on reddit. We have more blue kits than anything in this pairing, I just left out blue. I'll edit the original post.

 

[sryglet]

This is mom. Dad passed away unexpectedly a couple months back when his enclosure was crushed by a tree during a storm, and I am trying to find more recent pictures of him where me or one of my kids aren't holding him.

 

[sryglet]

Also to address the above, I copied and pasted a lot from the original post on my phone and had left out blue. We have had a lot of blue Japanese babies. I edited it to fix the mistake!

 

[sryglet]

I dont have pictures of all of them, but these were some of her litter mates as babies.

 

[MsTemeraire]

...I think she may have chinchilla light (also known as sable, <chl>) and one non-extension gene <e>, and on top she may be a self <aa>.
If both parents have a recessive gene on the C locus, and only one has non-ex on the E locus, that would give you only a 12.5% chance of a kit ending up with both things. If some other thing like aa is needed for this, the chance would be even smaller. Accounting for the luck of the draw it doesn't seem wild to me to see this for the first time after several pairings.

I'm leaning towards the presence of c(chl) too - and she is definitely self-based, but also carries non-extension, e. This is what gives the sooty shading on the nose, and occurs with both c(chl0 or c(chd) if they are aa e(j)e, so she still may be c(chd).

A possibility is that she has some kind of a somatic mutation which allows colours/genes that normally don't appear together to express, or she is a genetic chimera, where two eggs have fused together. This might also explain her somewhat masculine looks. But also make sure she really is a doe - a buck with a split penis will seem to be female until they start puberty, when the penis becomes more pointy, usually at about 12 weeks.

 

[sryglet]

I'm leaning towards the presence of c(chl) too - and she is definitely self-based, but also carries non-extension, e. This is what gives the sooty shading on the nose, and occurs with both c(chl0 or c(chd) if they are aa e(j)e, so she still may be c(chd).

A possibility is that she has some kind of a somatic mutation which allows colours/genes that normally don't appear together to express, or she is a genetic chimera, where two eggs have fused together. This might also explain her somewhat masculine looks. But also make sure she really is a doe - a buck with a split penis will seem to be female until they start puberty, when the penis becomes more pointy, usually at about 12 weeks.

Yes, I have kind of been obsessively checking to make sure she is a doe. She is definitely a doe unless she has a REALLY severe split penis, and we have never produced a buck with a split penis. She just has a massive, very blocky head.

What do you think about the markings appearing more and more over time?

 

[sryglet]

I'm leaning towards the presence of c(chl) too - and she is definitely self-based, but also carries non-extension, e. This is what gives the sooty shading on the nose, and occurs with both c(chl0 or c(chd) if they are aa e(j)e, so she still may be c(chd).

A possibility is that she has some kind of a somatic mutation which allows colours/genes that normally don't appear together to express, or she is a genetic chimera, where two eggs have fused together. This might also explain her somewhat masculine looks. But also make sure she really is a doe - a buck with a split penis will seem to be female until they start puberty, when the penis becomes more pointy, usually at about 12 weeks.

I have been thinking about the possibility of her being a chimera. I am just perplexed because we haven't produced sooty noses or any babies with any white on them. As you can see her parents' pairing typically produces somewhat decent harlequin markings. I am just confused about how these colors got in the bloodline at all, let alone were carried recessively?

 

[Naelin]

This is mom. Dad passed away unexpectedly a couple months back when his enclosure was crushed by a tree during a storm, and I am trying to find more recent pictures of him where me or one of my kids aren't holding him.

Damn, poor boy! That must have been horrible

or she is a genetic chimera, where two eggs have fused together. This might also explain her somewhat masculine looks.

I heavily doubt this is the case. Chimaeras have very clear splits on the parts made out of one and the other set of genes (See a rabbit example here, or this cardinal). Instead, this doe has a shaded point pattern that is diffuse and changes the places where she has colour as she molts (which definitely wouln't happen if this was the effect of chimaerism).

Other people have produced rabbits that have a similar aspect to this one by mixing a seal point with a harlequin (see the link in my previous post) so this just seems like a non-standard colour resulting of recessive chl propping up and being mixed with Harle. The effects of harlequin mixed with non-full-colour C genes seem to be very poorly documented. Maybe this will be my next project since I suddenly have a bunch of harles going around...

 

[Naelin]

I have been thinking about the possibility of her being a chimera. I am just perplexed because we haven't produced sooty noses or any babies with any white on them. As you can see her parents' pairing typically produces somewhat decent harlequin markings. I am just confused about how these colors got in the bloodline at all, let alone were carried recessively?

How they got in the bloodline is anybody's guess. Your pedigree only tells you what happened three generations back, you don't know what happened before that. From what I've read around, mixing a breed "just once" to improve a specific quality of another breed seems to be a somewhat common practice with rabbits. This is also not even necessary, since there isn't any particular need for harlequins to not have a recessive C gene, just to to have one full-colour or a chinchilla one.

How this was carried recessively is much easier to explain... they just do, because you can go a lot of generations without noticing a recessive gene, until just by luck of the draw you get two rabbits that were carrying recessives with enough luck to pass both down and make the recessive pop up suddenly. With breeds that only accept a very narrow variation of colours like Harlequin this is even easier. Chin light is recessive to both full colour and chinchilla (the two Cs accepted in the Harle breed), so it can hide in a Harlequin light essentially forever, or until by chance you mix two rabbits that happen to both have recessive chl, ch or c.

This is one of the neat differences between the breeding practices of rabbits vs dogs/cats: In dogs/cats, breeders try to "dilute" unwanted recessives by avoiding inbreeding as much as possible, because it is not common practice to really cull a breeder as soon as they show a negative recessive trait. In rabbits it's almost the opposite, it's encouraged to line breed (breed parent to child) in order to figure out recessive traits and either get those recessives showing, or removing them from the pool entirely by culling the breeders. Your two harlequins are probably unrelated enough (and not line-bred themselves enough) for that recessive trait to have been "diluted" and gone unnoticed for those many generations.

 

[sryglet]

How they got in the bloodline is anybody's guess. Your pedigree only tells you what happened three generations back, you don't know what happened before that. From what I've read around, mixing a breed "just once" to improve a specific quality of another breed seems to be a somewhat common practice with rabbits. This is also not even necessary, since there isn't any particular need for harlequins to not have a recessive C gene, just to to have one full-colour or a chinchilla one.

How this was carried recessively is much easier to explain... they just do, because you can go a lot of generations without noticing a recessive gene, until just by luck of the draw you get two rabbits that were carrying recessives with enough luck to pass both down and make the recessive pop up suddenly. With breeds that only accept a very narrow variation of colours like Harlequin this is even easier. Chin light is recessive to both full colour and chinchilla (the two Cs accepted in the Harle breed), so it can hide in a Harlequin light essentially forever, or until by chance you mix two rabbits that happen to both have recessive chl, ch or c.

This is one of the neat differences between the breeding practices of rabbits vs dogs/cats: In dogs/cats, breeders try to "dilute" unwanted recessives by avoiding inbreeding as much as possible, because it is not common practice to really cull a breeder as soon as they show a negative recessive trait. In rabbits it's almost the opposite, it's encouraged to line breed (breed parent to child) in order to figure out recessive traits and either get those recessives showing, or removing them from the pool entirely by culling the breeders. Your two harlequins are probably unrelated enough (and not line-bred themselves enough) for that recessive trait to have been "diluted" and gone unnoticed for those many generations.

Dad passing away was very sad. He was only just shy of four and just one leg shy of his GC leg, and was our three young children's first rabbit. He survived the cage being crushed (happened overnight, we weren't aware) and when I went out to care for everyone I had to free him with a chainsaw, which I'm assuming literally scared him to death. It was so sad. We only have a tiny herd and they are all beloved pets on top of breeders and show stock.

I am considering crossing her to a full brother (lilac) in a couple months just to see what colors she produces and help determine what exactly is being carried. We have a wait list of pet homes lined up.

Am I correct in assuming that these hidden genes could really mess up the offspring of my Japanese stock if they were crossed with magpie?

 

[Naelin]

You may be thinking of the dominance of the genes the opposite as it is, let me explain first how it works and then the answer will be more understandable:
Your doe's interesting markings are probably being caused by the C and the E locus.

The C locus changes the amount of black and yellow pigment that shows in your rabbit and has 5 variations: Full-colour "C", chinchilla dark "chd", chinchilla light/sable "chl", himalayan "ch" and albino/rew "c". Each one is completely dominant over the others in the same order I named them. What this means if that if I randomly combine any of those 5 options, the ONLY one that will show is the one that is first in that order.
For example I have chlch, the rabbit will only show the chl, and you wouldn't know it has ch.

The E locus is a bit more complicated, it changes how the black and yellow pigment gets "pushed" up or down each hair, goes in this order: Steel (Es), Full Extension (E), Japanese (ej) and non-extension (e).
It's harder to figure out in that Japanese (the one that causes harlequin) is incompletely dominant, meaning it can show through other things and other things can show through it (that's why you may hear about "harlequinised" torts for example)

The parents of your doe both had Full colour and something else, and probably Japanese and non-extension, but this was impossible to know until, by mere chance, one of the kits got both copies of that "something else" in both genes.
When you cross her, she will only pass one copy of what she has (let's assume chl and e) and the male will pass down a copy of what he has. If the copy he passes down is dominant over what she has, her genes will get hidden again in the next generation. The only way to keep them visible is by being paired to something more recessive.

With all that said:

I am considering crossing her to a full brother (lilac) in a couple months just to see what colors she produces and help determine what exactly is being carried. We have a wait list of pet homes lined up.

Crossing her with a full colour wouldn't help in this case, because the full colour C would hide whatever she has in that locus. The more very recessive genes the sire has, the more it will help to determine what she has. If you happen to have any rew (cc) or himalayan (ch_) to cross her with that would be ideal. Better yet if that sire is self-based and/or non-extension.

Am I correct in assuming that these hidden genes could really mess up the offspring of my Japanese stock if they were crossed with magpie?

Nope. Magpie is nothing other than japanese + chinchilla dark, and chinchilla dark (chd) is dominant over chinchilla light (chd), so whatever thing she passes down in the C locus will be overridden by the chinchilla gene of the magpie if he has both chin genes (what could happen is that whatever she carries shows if the magpie sire also happens to be carrying chl, ch or c in the second gene, which would actually be helpful to determine if that magpie sire is carrying those things. If everyone comes out as magpie, you know for a fact that he's chdchd)
In fact if you breed her to any other regular harlequin, whatever she has going on will just be "hidden" again, being carried unsuspected for someone else to wonder what the hell is going on many generations down the line


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If i was in your position and trying to figure out her genes, I will cross her with males that have as close as possible to these genes (doesn't need to be all at once, you can determine each gene one by one): aa__ch___ee. (So a self-based extended himalayan, essentially a Californian with a white tail)
Since that male would be full of the most recessive genes possible (other than rew) in the locuses that we don't know, whatever shows through is necessarily a gene that she passed down. So:
-If you get all agoutis, you know she has AA. If some are agouti and some are self, she is Aa
-If you get any full color, scrap everything because something is wrong (potentially the male being Es instead of ee, that's a whole other can of worms)
-If you get chinchillas, her C locus is actually chd. If you get sable, you confirm she's chl.
-If you get ONLY sable, she's chlchl. If there are any himalayan or rew in the mix, she's chlch or chlc
-If they are all harlequin/harlequinised, she's ejej (I doubt it). If some are full extension she's Eej, and if some are non-extension, she's eje.