From owner-drosophila@net.bio.net Sat May 14 23:00:00 1994 Newsgroups: bionet.drosophila Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!pbmac-5.ucdavis.edu!user From: tdlong@ucdavis.edu (Tony Long) Subject: Re: RAPDs with Drosophila Message-ID: Followup-To: bionet.drosophila Sender: usenet@ucdavis.edu (News Guru) Organization: Center for Population Biology References: <9405131441.AA14618@andy.bgsu.edu> <1994May14.143852.10635@iitmax.iit.edu> Distribution: bionet Date: Sun, 15 May 1994 19:21:22 GMT Lines: 50 In article <1994May14.143852.10635@iitmax.iit.edu>, garfinkl@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@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@ucdavis.edu .