Dear Maize Geneticists:
As one part of our NSF Plant Genome project
(http://www.nsf.gov/cgi-bin/showaward?award=9975868) we will be
developing 500 PCR-based, high-throughput, allele-specific, genetic
markers. Because the resulting markers yield +/- scores it will not
be necessary to conduct electrophoresis to obtain genotypes. These
markers are based on the indel polymorphisms (IDPs) that occur at
high frequencies in introns and UTRs of maize alleles.
To design IDP markers for a given gene we design primers to amplify
the corresponding introns/UTRs from B73 and Mo17. Automated sequence
alignments define IDPs. Then primers corresponding to these IDPs are
designed (using a new automated primer design tool that is under
development) and tested.
This process necessarily requires a large number of introns and UTRs
as a source of IDPs. Towards this end we and others are obtaining 3'
sequence data for maize ESTs. In addition, we expect to ultimately
be able to "harvest" introns of predicted genes found in the
Mu-flanking sequences that will be generated by the Stanford et al
maize genome project funded by NSF last year. Predicted gene
structures will be determined in these sequences using the
SplicePredictor program
(http://gremlin3.zool.iastate.edu/cgi-bin/prg/sp.cgi) developed by
Volker Brendel (Iowa State Univ), a member of the Stanford project
team. But in the meantime we are relying on those maize genes that
have been deposited in GenBank. Unfortunately GenBank currently
contains only about 150 maize genes (as opposed to cDNAs or ESTs
which of course do not include introns).
Hence, this request:
Please send us genomic and cDNA sequences from your genes. We will
use your sequences to identify IDPs between the B73 and Mo17 alleles
of your gene and then develop IDP markers which will be genetically
mapped in the IBM (intermated B73 x M017) RI population. Hence, if
you have not yet mapped your gene this step will generate that
information at no additional cost or effort to you.
The sequences you send need not be complete. We can handle partial
cDNAs or incomplete genomic sequences as long as they define at least
one intron.
We will not release your sequences per se, but to be useful to the
community it will be necessary that we release the IDP primer
sequences that amplify your gene. Please contact me if you have
concerns about this release policy. The goal is to create a resource
for our community and we need your help. Hence, we'll try to be as
flexible as possible.
If you are willing to contribute to this effort, please fill in the
following form and e-mail it back to me (send only one gene per
e-mail message and PLEASE do not send genes that have already been
deposited in GenBank):
Contact information (who you are and how we can reach you):
Gene name/designation (this can be "coded" if you so desire):
Genomic sequence:
cDNA sequence:
Please indicate the genetic map position of your gene (if known):
thanks very much,
Pat
Patrick S. Schnable
Director, Center for Plant Genomics
Director, Center for Plant Transformation & Gene Expression
Professor of Plant Genetics
G405 Agronomy Hall
Iowa State University
Ames, IA 50011 USA
schnable at iastate.edu
515-294-0975 (office)
515-294-2299 (fax)
http://www.public.iastate.edu/~schnable/http://www.plantsciences.iastate.edu/
