Need help understanding color genetics

[HosDucks]

So I have read over the following articles on color genetics multiple times:
https://www.backyardchickens.com/articles/mallard-derived-duck-color-genetics-basics.74277/
http://www.nantahala-farm.com/ancona-dave-holderread-waterfowl-genetics-s.shtml
http://www.nantahala-farm.com/ancona-duck-colors-genetics-s.shtml
http://www.nantahala-farm.com/ancona-duck-colors-genes-s.shtml

While these articles have cleared up a ton of information for me, I am still a bit lost when it comes to how the sex-linked genes of Chocolate and Buff pass down.

I understand the fact that these genes are located on a part of a chromosome that female ducks only have one of, thus the reason why they only need one gene marker of the recessive gene to show...because they only one one loci for it.

What I don't understand is how that translates to how the genes are passed down. According to Dave Holderread, when a black Drake breeds with a Chocolate duck, all of their offspring ought to be black. When the reverse is done, a Chocolate Drake to a Black Duck, the result is all female offspring are chocolate, and all male offspring are black. No matter how many times I work out the punnet squares, I can't get the result. I can use modified parameters to make the Chocolate Drake x Black Duck result match; however the same modification doesn't show the the same result for a Black Drake x Choc duck to match.

What information am I missing (or more likely just not understanding) for figuring out the theoretical chances of coloration of offspring, with regards to the sex-linked genes.

 

[Quatie]

In ducks, the sex chromosome are called Z and W. Drakes are ZZ, while hens are ZW. The chocolate gene is sex linked and found on the Z gene. The chocolate gene is recessive. While most genes you would require two recessive genes for the phenotype to appear, the females only need one copy of the chocolate gene since they only have one Z chromosome.

So if a drake is a chocolate, he has two recessive chocolate genes. Zch Zch. If you cross him with a non chocolate hen, ZCH W, the female will provide the W chromosome to the hens and the Drake will provide the chocolate color gene, give you Zch W. The drakes will get the ZCH from the hen and Zch from the Drake. So all the Drakes will be ZCHZch, heterozygous for the chocolate gene. Because the chocolate gene is recessive, the chocolate color will not present it self.

Hopefully that makes the chocolate gene make more sense.

 

[HosDucks]

In ducks, the sex chromosome are called Z and W. Drakes are ZZ, while hens are ZW. The chocolate gene is sex linked and found on the Z gene. The chocolate gene is recessive. While most genes you would require two recessive genes for the phenotype to appear, the females only need one copy of the chocolate gene since they only have one Z chromosome.

So if a drake is a chocolate, he has two recessive chocolate genes. Zch Zch. If you cross him with a non chocolate hen, ZCH W, the female will provide the W chromosome to the hens and the Drake will provide the chocolate color gene, give you Zch W. The drakes will get the ZCH from the hen and Zch from the Drake. So all the Drakes will be ZCHZch, heterozygous for the chocolate gene. Because the chocolate gene is recessive, the chocolate color will not present it self.

Hopefully that makes the chocolate gene make more sense.

So if I understand it correctly, then I can look at the potential offspring as so:
- For the sex-linked genes (in this case Chocolate), the females can only inherit a gene from the Drake.
- For a male offspring, you run the probability normally, except for the fact that he will always get the one gene from his mother, and one of two inherited from his father.

So in the case of black drake and chocolate hen, we have two possible outcomes, depending on if the drake is homozygous or heterozygous for the dominant NON-chocolate gene.
1) ZCh ZCh x Zc W: all females are ZCh W (black) and all males are ZCh Zc (black and heterozygous for the chocolate gene)
2) ZCh Zc x Zc W: Females have a 50/50 chance of being ZCh W (black) or Zc W (chocolate). Males also have a 50/50 of being ZCh Zc (black) or Zc Zc (chocolate)

So assuming that I understood you and the above is correct, then I think I have the genetics of color down pretty good now. How the sex-linked genes were being passed down had me a bit baffled. With the way you used the 'W' to represent the "missing" gene, actually helped me quite a bit. And assuming that I am correct in understanding that the Hen will always pass on the 'W' to her female offspring and her other gene (either ZCh or Zc, depending on her genetics) will always be passed on to her male offspring, then I do get it now.

Feel free to correct me if I'm wrong on any of this. And thank you for your help and explanation.

 

[Quatie]

So if I understand it correctly, then I can look at the potential offspring as so:
- For the sex-linked genes (in this case Chocolate), the females can only inherit a gene from the Drake.
- For a male offspring, you run the probability normally, except for the fact that he will always get the one gene from his mother, and one of two inherited from his father.

So in the case of black drake and chocolate hen, we have two possible outcomes, depending on if the drake is homozygous or heterozygous for the dominant NON-chocolate gene.
1) ZCh ZCh x Zc W: all females are ZCh W (black) and all males are ZCh Zc (black and heterozygous for the chocolate gene)
2) ZCh Zc x Zc W: Females have a 50/50 chance of being ZCh W (black) or Zc W (chocolate). Males also have a 50/50 of being ZCh Zc (black) or Zc Zc (chocolate)

So assuming that I understood you and the above is correct, then I think I have the genetics of color down pretty good now. How the sex-linked genes were being passed down had me a bit baffled. With the way you used the 'W' to represent the "missing" gene, actually helped me quite a bit. And assuming that I am correct in understanding that the Hen will always pass on the 'W' to her female offspring and her other gene (either ZCh or Zc, depending on her genetics) will always be passed on to her male offspring, then I do get it now.

Feel free to correct me if I'm wrong on any of this. And thank you for your help and explanation.

You got it correct!

 

[HosDucks]

You got it correct!

Awesome thanks a lot. That was a great help.

Now a few more questions:
- From reading Dave Holderread's stuff, I now assume that tricolor Anconas are basically Anconas without the extended black gene (homozygous for the recessive wild-type gene at that loci). Is this a assumption correct?

-Assuming the above is correct, what happens to ducks that are chocolate, but do not have the extended black gene? Does it still lighten any black feathers it may have, or does the chocolate gene only take effect on plumage that been effected by the extended black gene?

-Similarly to the above question, do the blue gene(s) effect pretty much any plumage (except for on white duck, since a homozygous white overrides all feather pigmentation)?...Therefore you can have things like a Blue Mallard pattern, silver Mallard pattern, etc.

-It seems most people view the extended black gene as a simple Dominant/recessive gene, that is, a homozygous black duck appears the same as a heterozygous black duck...as opposed to how the blue gene has a stacking effect (blue vs silver, lavender vs lilac, etc). Dave Holderread seems to have an opposing view to this however, at least from the way I read it. He seems to view heterozygous black as leading to the true plumage pattern of an "pure Ancona" and that if a duck is homozygous for ext. black, then it would actually have more black coverage, and would have a "Magpie" pattern. Is there any consensus on to which is correct?

-Are any other genes known to stack if they are homozygous, similar to the blue gene? The bibbed gene? The runner pattern gene?

 

[Quatie]

I am not familiar with the ancona genetic pattern. This article may be helpful. It talks a lot about the various genetics.

https://www.backyardchickens.com/articles/mallard-derived-duck-color-genetics-basics.74277/

I am not aware of other genes that stack in Mallard derived ducks. I haven't jumped too much into the mallard genetics. I have been more interested in the muscovy color genetics. Chocolate works the same in both species.

@Pyxis who wrote that article may be able to answer more of your questions.

 

[Pyxis]

- From reading Dave Holderread's stuff, I now assume that tricolor Anconas are basically Anconas without the extended black gene (homozygous for the recessive wild-type gene at that loci). Is this a assumption correct?

This would make sense, yes. From what I've read, that's also what I think.

-Assuming the above is correct, what happens to ducks that are chocolate, but do not have the extended black gene? Does it still lighten any black feathers it may have, or does the chocolate gene only take effect on plumage that been effected by the extended black gene?

Chocolate still dilutes black even on mallard base Nutmeg Calls are chocolate mallard, genetically. Gold Phase welsh harlequins are chocolate - that is the only difference between them and Silver Phase.

-Similarly to the above question, do the blue gene(s) effect pretty much any plumage (except for on white duck, since a homozygous white overrides all feather pigmentation)?...Therefore you can have things like a Blue Mallard pattern, silver Mallard pattern, etc.

Yes. Again to use Calls, Blue Fawn is one copy of blue on mallard base. Pastel is two copies. Butterscotch is two copies plus Light Phase.

-It seems most people view the extended black gene as a simple Dominant/recessive gene, that is, a homozygous black duck appears the same as a heterozygous black duck...as opposed to how the blue gene has a stacking effect (blue vs silver, lavender vs lilac, etc). Dave Holderread seems to have an opposing view to this however, at least from the way I read it. He seems to view heterozygous black as leading to the true plumage pattern of an "pure Ancona" and that if a duck is homozygous for ext. black, then it would actually have more black coverage, and would have a "Magpie" pattern. Is there any consensus on to which is correct?

I think Extended Black is incompletely dominant. It's why one copy makes the Ancona pattern, while two makes Magpie.

It's also why you can get 'bleed through' of brown on a duck with only copy. Like this one:

-Are any other genes known to stack if they are homozygous, similar to the blue gene? The bibbed gene? The runner pattern gene?

What you mean here are incompletely dominant genes, like I was just talking about with extended black. Blue is one, of course. Runner pattern is another, yes. That's it in mallard-derived ducks.

Bibbed isn't its own gene, it's linked to to extended black. Well, there IS a recessive bibbed gene, which is how you can get bibbed mallard colors, but that one is a different thing and is purely recessive.

 

[HosDucks]

Thanks for all the info Pyxis, it all helps a lot. I have one more question (for now at least, lol).

In regards to the color phase alleles, I see you list Li+ (dominant wild-type), li (light phase) and li^h (harlequin). Which is more dominant between li and li^h?

 

[Pyxis]

In regards to the color phase alleles, I see you list Li+ (dominant wild-type), li (light phase) and li^h (harlequin). Which is more dominant between li and li^h?

If you have them both on the same bird, they express together They make a color called Spot.