Genetic Marker Survey

AAtDB Data Submission Address Curator at FRODO.MGH.HARVARD.EDU
Thu Sep 10 01:25:48 EST 1992


September 8, 1992

Dear Colleague:

    Your help is needed to update the linkage map of Arabidopsis. The
maps currently available through AAtDB (An Arabidopsis thaliana
Database established by Mike Cherry, Sam Cartinhour, and Howard
Goodman) and being developed with AIMS (Arabidopsis Information
Management System database established by Sakti Pramanik and Randy
Scholl) need additional input from the community to remain current.
The attached forms will be used to produce new lists of mapped visible
and molecular markers for use by the Arabidopsis community. Complete
recombination data will be requested later when a decision is made
concerning the optimal format for producing future genetic maps. This
initial request is simply for general linkage and mapping information.
Results will be added immediately to both AAtDB and AIMS and
distributed in tabular form through the electronic network by November
6th. We hope to have this information available for distribution at
the Plant Genome Conference (November 9-11, San Diego, CA) to
demonstrate the extent of recent advances in Arabidopsis mapping
projects and facilitate planning and coordination of future mapping
programs.

    The success of this effort will obviously depend on your
willingness to provide data. Please make an effort to respond. Even
preliminary data indicating linkage to a single marker would be useful
for this initial survey. We realize that in some cases, individuals
may be reluctant to submit detailed mapping information prior to
publication. This concern may be particularly evident when walking
efforts are in progress. It should nevertheless be possible to provide
approximate locations of mutant genes without jeopardizing research
efforts of individual laboratories. We plan to establish a system that
will allow individuals to submit mapping information and recombination
data to centralized locations for rapid dispersal to the Arabidopsis
community. Your help is needed to make this effort successful.

    We are also concerned that the same gene symbol may in some cases
be assigned to unrelated mutant genes. This will obviously lead to
confusion if the duplication is not detected before publication. We
need a continuously updated list of gene symbols that can be consulted
when you want to name a new class of mutants. We therefore hope that
you will return the form requesting information on new gene symbols
even if you do not have mapping information to contribute.

    Please respond by October 15 so the information can be compiled
and distributed without delay. This survey is being distributed in
two different ways to the Arabidopsis community: (1) through this
electronic network; and (2) by postal mail to individuals selected
from the mailing list for the Arabidopsis Biological Resource Center
at Ohio State. To respond by postal mail, completed forms should be
sent to: Arabidopsis Biological Resource Center at Ohio State; 1735
Neil Avenue; Columbus, OH 43210, USA (FAX 614-292-0603).
Alternatively, you may respond through email to the electronic version
of this survey by contacting AAtDB at: curator at frodo.mgh.harvard.edu.
This survey was prepared by David Meinke with assistance from Randy
Scholl, Maarten Koornneef, Elliot Meyerowitz, Joe Ecker, Chris
Somerville, and Mike Cherry.

Instructions for Completing Arabidopsis Mapping Survey

Please return completed forms to AAtDB through electronic mail using
the address: curator at frodo.mgh.harvard.edu. Alternatively, you can
print out this message or use the printed survey and return your
information to the ABRC postal address or FAX number given above.

Deadline for Receipt of Forms: October 15.

    Late forms will not be included in tables distributed through
electronic networks or presented at the Plant Genome Conference in San
Diego (November 9-11, 1992).

Use Form #1 to provide information on the approximate chromosomal
            locations of mutant genes mapped relative to visible or
            molecular markers. Information is requested for mutants
            not on the attached AAtDB list, and mutants on the AAtDB
            list but without mapping data.

Use Form #2 to provide information on the approximate chromosomal
            locations of cloned genes and other molecular markers.
            Information is requested for markers not on the attached
            AAtDB list, and markers on the AAtDB list but without
            mapping data.

Use Form #3 to provide information on the mutant gene symbols
            currently being employed in your laboratory. Please limit
            this list to symbols not on the enclosed AAtDB list.
            Please include only mutants that have been characterized
            in detail. We do not want to clutter this list with
            mutants that have simply been observed in passing.



Explanation of Form #1 (Mutant Genes):

Mutant Symbol: Standard 3-letter symbol and locus number where
               possible. (Example: abi3; emb28; tt5). Do not list
               alleles separately.

Full Name:     Complete descriptive name for the abbreviated mutant
               symbol. (Example: ABA insensitive; embryo defective)

Linkage Group:  Self explanatory.

Marker Tested: Most closely-linked visible or molecular marker tested.
               This marker should preferably be on the enclosed AAtDB
               list.

P ...........: Recombination % between mutant gene and most
               closely-linked marker noted in previous line.

               Note: Use (-) if you have demonstrated linkage to a
                     specific chromosome but choose not to provide
                     recombination data.

SD ..........:  Standard deviation for recombination estimate.

A/B .........: A: Locus appears to be ABOVE the tested marker on
                  linkage map.
               B: Locus appears to be BELOW the tested marker on
                  linkage map.

               Note: Use (-) if orientation of mutant gene relative to
                     tested marker has not been resolved.

Other Markers: Number of additional markers on the same chromosome for
               which you have recombination data. Use M for molecular
               markers; V for visible markers. Example: 2V indicates
               that recombination data are available for 2 other
               visible markers on the same chromosome; 4M indicates
               that recombination data are available for 4 other
               molecular markers on the same chromosome. Use ++V
               and/or ++M if the number of markers is greater than 5.



Additional Information - Form #2 (Molecular Markers).

Note: This form is not designed to collect information on YAC clones
      or contigs. The purpose is to place new markers on the genetic
      map.

Marker Symbol:  Abbreviated symbol for molecular marker.

Type of Marker: RFLP, RAPD, cDNA, cloned gene, microsatellite, or
                other.

Ecotypes:       Ecotypes used to identify molecular polymorphisms.




Examples of Proper Format

Form #1

Mutant Symbol             : emb9
Full Name of Mutant Gene  : embryo defective
Linkage Group             : 5
Marker Tested             : tt3
P                         : 1.6
S.D.                      : 0.7
A/B                       : -
Other Markers             : 2v


Form #2

Mutant Symbol             : XXXX
Type of Marker            : RFLP
Ecotypes                  : ws x ler
Linkage Group             : 5
Marker Tested             : tt3
P                         : x.x
S.D.                      : x.x
A/B                       : -
Other Markers             : 1v 2m


Form #3

New Marker Gene Symbol    : bio
Full Descriptive Name     : biotin auxotroph




Additional information for electronic survey form.

Please add your information as specified in the above examples using 


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