Suggestions for Separating and Reintegrating Breeding Groups?

This is all so fascinating. Will a barred hen paired with a blue Wheaton roo produce sex links?
I don't know. There are two requirements to make a sex link that you can tell sex at hatch. First the parents have to have a sex linked trait that you can see at hatch with the mother having the dominant one and the father having the recessive one at both genes at that gene pair. Your pairing has that. The mother has the dominant barred gene and the father has the recessive not-barred. All boys will be barred, none of the girls will be.

The other requirement is that you have to be able to see the difference at hatch. With barring that is a spot on the head of the boys and no spot on the girl's head. Some genetics are better at showing that spot in the down. Wheaton is one of the worst in that. So it's possible you could see it but I'm not sure. Even if that barred hen is black barred I'm not sure.

You just said a barred hen, you did not specify which. A Delaware hen is barred and has silver. If your Blue Wheaton is pure for gold, they would make red sex link chicks. The genetics need to line up just right to make a sex link.

The Blue in the Blue Wheaton doesn't mean anything as far as sex links. Blue just modifies what would normally be black to that blue shade. A Blue Australorp would be a solid black bird if not for the blue. Not so for your Wheaton.
 

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