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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