Request for support for a grant to NIH for mapping

Susan Dutcher dutcher at genetics.wustl.edu
Fri Oct 8 12:43:20 EST 2004


Dear Members of the Chlamydomonas community and interested others:

Thanks to the pioneering work of Carolyn Silflow and Pete Lefebvre, the 
Chlamydomonas community has a physical map that tethered to the genetic 
map.  Yet there is still a need for a denser map to facilitate the 
positional cloning of mutant alleles that do not have a tag.  The 
availability of the draft genome sequence has made this easier, but it 
still requires some effort.  Dr. Ray Miller at Washington University, 
who was one of the original scientists involved in SNP mapping in the 
human genome, is writing a grant to do SNP mapping in Chlamydomonas.  
The grant will have three aims.  The aims are:
1). To construct a dense genetic map of Chlamydomonas by genotyping 
single nucleotide polymorphisms (SNPs) on 200 recombinant strains (137 X 
S1D2).  The map will help to anchor and orient contigs from the draft 
sequence, which makes this sequence more useful,
2).  To construct a fingerprint map of the Lefebvre BAC collection to 
use for orienting contigs (at the Washington University Genome 
Sequencing Center),
3).  To assemble collections of meiotic progeny from mutant strains and 
genetically map the location of the mutations at a fine scale with high 
throughput methods using bulked segregants.  This collection of mutants 
will be of two kinds.  First, mutants in the Chlamydomonas Genetics 
Center will be crossed to S1D2 and the mutations will be mapped.  We 
will make the data publicly available as it obtained.   Based on similar 
experiments in C. briggisae that Ray has undertaken with this community, 
it should take about 2-3 days to map the mutant once the meiotic progeny 
have been isolated and phenotyped (3-4 weeks).  He will use similar 
techniques to map mutants found by the community.  Anyone that wants a 
mutant mapped would send it and have the information within a month.

Simply put, the goal will be to have a funded resource for generating a 
map and provide mapping data for more rapid positional cloning of new 
Chlamydomonas mutations, taking advantage of bulk segregant mapping that 
Ray has developed in C. elegans with Bob Waterston.  He has recently 
submitted a grant to set up this type of facility for the C. briggisae 
community. 

I am writing to you because this proposal will only be funded if Ray has 
community support.  Ray submitted this grant last March, but it was not 
funded.  The science was well received, but he had almost no community 
support and they were worried about how much use the facility would 
have.  I think this would be a great resource for the community and each 
of us individually. Ray has spoken to Dan Rokhsar at JGI who urged him 
to pursue the grant, as the fingerprinting and map will greatly aid the 
draft genome assembly.   My role would be to train a technique to mate 
the mutants, phenotype and make DNA.  Ray would take over from that 
point.  

If you are interested, please send an email or letter
1.) voicing your support and
2.) describing the kinds of mutants that you would study using the 
facility and why they are interesting to NIH.
 
This grant will be submitted to the Human Genome Study Section as a 
revised proposal on November 1.  Please send letters and emails as 
quickly as possible.  Please contact me (dutcher at genetics.wustl.edu)  if 
you have questions.


                    Best wishes


                    Susan Dutcher

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