I am wondering if it is possible to outcross a duplication?
I have a mutant that has a deletion of ~600bp but has a wild-type copy (confirmed by PCR). I need to have only the deletion in the worm and not the wt copy!
Has anyone had success/know if it’s possible to outcross to eliminate a wt copy and leave only a deletion? I guess this is dependent on the distance of the wt copy from the deletion and I’m not sure of the distance between them. Any advice would be helpful!
It depends greatly on whether your duplication is tightly linked to the original locus. Probably the easiest thing is to outcross your deletion allele a few fold with a trans balancer (a translocation or maybe a flanking Dpy Unc) and see whether your duplication comes along for the ride. You could also outcross using PCR detection of your deletion, assuming that you can detect it independently of the duplication. That is actually best, since you don’t select against outcrossing the Dp if it is closely linked.
I don’t know the odds of a duplication being nearby (I’d assume it is greater than random, but I don’t know that for a fact). But if it is nearby your problem becomes much greater. If so, you’ll need to find out where your Dp lies in the genome. Hmm, I’d have to think about that.
- If your Dp contains a SNP not contained in your deletion, you could map it that way against SNPs in the region…
- You may also want to check out DNA flanking the Dp insertion site (this will give you exact location information). This may mean mapping the extent of your Dp with PCR, then doing inverse PCR to detect flanking DNA. But it bears more thought.