RAPDs with Drosophila

Tony Long tdlong at ucdavis.edu
Sun May 15 14:21:22 EST 1994

In article <1994May14.143852.10635 at iitmax.iit.edu>, garfinkl at iitmax.iit.edu
(Mark D. Garfinkel) wrote:
> 	I have little doubt that (CA)n-containing interspersed micro-
> satellite repeats of the type found in mammalian DNA are also present in
> the Drosophila genome. That they may be useful as polymorphic markers is
> supported by Kafatos' use of (CA)n-repeats to make a X-chromosome linkage
> map for the malaria vector Anopheles gambiae (1993, Science 261: 605-608).
> -- 
> Mark D. Garfinkel (e-mail: garfinkl at iitmax.acc.iit.edu)
> My views are my own, which is why they're copyright (c) 1994

		I am hoping we can draw Steve Schaeffer into this discussion.  I don't
think there is a great deal of evidence for microsatellites in D.
melanogaster at the level seen in other organisms.  There is a great deal
of population genetics work done on Drosophila by the likes of Aquadro,
Aguade, Kreitman, Langley, Schaeffer etc ..  Most of these studies have
looked at variation between a number of 'wild' chromosomes at the level of
6 - cutter, 4 - cutter (restriction enzymes) or sequence variation.  There
is very little insertion/ deletion variation at intermediate frequencies
(this is how a polymorphic NN repeat would be manifested), and most small
deletions/insertions are not simple repeats.  Of course this does not imply
there isn't this sort of variation (for examples the period gene), just
that it hasn't been observed much so far.  Don't get me wrong, I do hope
someone looks in a genomic library for such microsatellites.

		A better way (IMHO) that we have used to generate polymorphic markers is
to make oligonucleotide primers that amplify small (200 - 400 bp) parts of
introns and then run these products under SSCP conditions.  This is
expected to often result in codominant markers between lines (and has). 
Alternately larger fragments can be amplified and restricted to give
products in the size range suitable for SSCP (see a paper on mapping a male
sterility factor by the Wu group in Genetics about a year ago).  One big
advantage of this is that it doesn't involve the initial work required to
generate a number of microsatellite markers.  The added advantage, is that
the physical location of the marker is known (from the in situ often done
by the group who sequenced the gene).  Conversely, if one needs genetic
markers in certain region they can be created almost at will (for about one
hour of time on Gopher and Genebank -- less once the FLYBASE consortium
move to the next phase!), as so many genes (usually cDNA's) have been
sequenced in D. mel (although unfortunately, not so many genomic sequences
are available). 

Tony Long
Center for Population Biology
U. C. Davis
Davis, CA
tdlong at ucdavis.edu

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