deletion mapping by PCR?

[Christopher Shaffer]

Hello Fellow Drosophilists:

I am about to embark on a deletion mapping project in which 
I need to map about 25 deletions for the presence or absence of
my cDNA clone.  The standard technique would be to take each
deletion stock, outcross it to a pericentric inversion to 
increase the likelyhood of asynapsis and do in situ squashes
on 3rd instar salivary glands, throw out 1/2 the slides that are not
pericentric inversion over deletion and then do in situ hybridizations
to the polytene chromsomes.  Needless to say, not a small amount of
work.

I would like to try a simpler approach.  I am sure others have thought
of this and would, therefore, have worked the bugs out of the system. The
idea is to use a suitable embryonic marker which would allow one to
collect embryo's homozygous for the deletion chromosome.  These embryos
could then be used in a PCR based assay looking for the presence of the
gene.  If anyone has tried this technique I would appreciate any
pointers.  For example, what embryonic marker to use? I was thinking a
"blue balancer" wold be nice if it expressed b-gal early enough and
you could still get "PCR-able" DNA from embryo's that had gone though a
b-gal staining assay.

If you have a protocol or just advise please drop me a line.

Christopher Shaffer Ph.D.                   Phone:(314) 935-6837
152 McDonnell Hall                          Fax:  (314) 935-5125
Campus Box 1229                             shaffer at biodec.wustl.edu
Washington University
St. Louis MO 63130