Important Request

DAVID W MEINKE meinke at osuunx.ucc.okstate.edu
Wed Mar 18 19:43:42 EST 1998


Dear Colleagues:

Two years ago I requested community input to summarize linkage
data for mutant genes of Arabidopsis and revise the classical
genetic map.  That survey resulted in the current version of the
map available through AtDB and my WWW home page.

The time has come to update this information for the Arabidopsis
community.  The revised map will be made available through AtDB,
featured in future publications, and used to promote continued
advances in the Multinational Arabidopsis Genome Research Project.

Please give this survey your immediate attention.  The results
should be quite impressive if the entire community participates.
Note that this request deals only with MUTANT genes, not cloned
genes for which a mutant phenotype has not been established.

Your response is requested by April 15 or sooner if possible.
This should provide enough time to create an updated map for
distribution at the Madison meeting in June.  Please submit here
any information you plan to present at that meeting.

I will send periodic reminders to encourage wide participation.
This survey is part of a coordinated effort to standardize genetic
and physical mapping data for Arabidopsis.  Your contribution is
greatly appreciated.

Sincerely,

David Meinke
Co-curator (with Maarten Koornneef) of the classical genetic map

________________________________________________________________

Please use these steps to submit information on gene symbols and
estimated map locations of mutant genes.  The following URL sites
are referenced.

USE SITE #9 FOR QUICK NAVIGATION TO OTHER SITES LISTED HERE:

#1: http://mutant.lse.okstate.edu (Home Page)
#2: http://mutant.lse.okstate.edu/genepage/publinks.html
#3: http://mutant.lse.okstate.edu/symbols_dir.html
#4: http://mutant.lse.okstate.edu/front_mutant/formsexpl.html
#5: http://mutant.lse.okstate.edu/linkage_dir.html
#6: http://mutant.lse.okstate.edu/genepage/mutant_list_exp.html
#7: http://mutant.lse.okstate.edu/front_mutant/formsexpl.html
#8: http://mutant.lse.okstate.edu/genepage/classical_map.html
#9: http://mutant.lse.okstate.edu/navigation.html

1. If you are unfamiliar with community standards for Arabidopsis
genetics, please refer to the recent publication on this topic by
Meinke and Koornneef (Plant Journal 12:247-253).  The text can be
found on the WWW at Site #2.  Please follow procedures outlined in
this publication.

2. When selecting a name for a mutant isolated in your laboratory,
you should choose a mutant gene symbol that does not conflict with
existing symbols.  The current list of mutant gene symbols can be
found at Site #3.  Please check this list.  It should include all
mutants being studied in your laboratory.

3. New symbols for mutant genes can be reserved by sending an
email message to David Meinke at: meinke at osuunx.ucc.okstate.edu,
by completing the survey below, or by completing a form available
at Site #4.  Please submit information on new symbols immediately.

4. Linkage data for mutant genes of Arabidopsis are summarized in
a table available at Site #5.  This table should include every
mutant gene for which linkage information is available.  An
explanation of column headings is provided at Site #6.

Please check carefully the information included in this table and
make additions/corrections on the form provided or by completing
the form below.  The information included in this table will be
used to construct the revised genetic map of visible markers.

If you wish to submit linkage/map information via the WWW, please
complete the form available at Site #7.

5. The outdated classical genetic map can be viewed in text format
at Site #8.  Please note any changes that need to be made in the
locations and orientations of mutant genes inlcuded on this map.
__________________________________________________________________

If you prefer to respond to this email message rather than access
forms available through the WWW, please complete the survey below
and return to David Meinke at: meinke at osuunx.ucc.okstate.edu
__________________________________________________________________

SECTION # 1:

Please note here any corrections/additions to the List of Mutant
Gene Symbols.  Refer to WWW Site #3 for current list.  Repeat this
form if necessary for multiple symbols.

New Gene Symbol (3 letters in CAPS):
Full Descriptive Name for Symbol:
Name of Reference Laboratory:
Mutant Class if not Obvious from Symbol:
# Different Genes Associated with Symbol:
Chromosomal Location if Single Mutant Gene:
Correction Requested for Existing Symbol:
Additional Comments:
__________________________________________________________________

SECTION #2:

Please note here any corrections/additions to the Linkage Table of
Mutant Genes.  Refer first to WWW Site #5 for the current table,
which serves as the basis for the genetic map.  Then consult the
detailed instructions that follow the form below.

Locus:
Chromosome:
Reference lab:
Map status:
Classical Map Data:
   Map location:
   Linked marker:
   Recombination %:
   Above/below:
Molecular Map Data:
   Map location:
   Linked marker:
   Recombination %:
   Above/below:
Physical Map Data:
   Anchored clone:
   Linked marker:
   Estimated distance:
   Orientation:
__________________________________________________________________

INSTRUCTIONS FOR SECTION #2:

BACKGROUND:  The classical map was originally built using genetic
distances based on recombination frequencies with visible markers.
Other mutant genes were later cloned and placed on the recombinant
inbred (RI) map or assigned a position relative to molecular
markers on the RI or physical maps.  The approximate locations of
these mutant genes can still be noted on the classical genetic map
if the molecular markers used for reference are included on the RI
map.  The major function of the classical genetic map is to show
the approximate locations of genes identified by mutation.
Absolute locations will eventually be revealed by sequencing the
entire genome.

LOCUS:  Your gene symbol and locus number. Please use CAPS.

CHROMOSOME NUMBER:  Self explanatory.

REFERENCE LAB:  Lab responsible for producing the map data.

MAP STATUS:  Use one or more of the following symbols:

   CM:  Location established on classical genetic map.

   RM:  Location established on recombinant inbred map.

   PM:  Location established on physical map.

   AV:  Approximate location determined by recombination data with
        visible markers.

   AM:  Approximate location determined by recombination data with
        molecular markers.

   AVM: Approximate location determined by recombination data with
        both visible and molecular markers.

   LO:  Assigned to linkage group only.  Insufficient data to
        estimate location.

   U:   Nature and extent of mapping data unresolved.

CLASSICAL MAP DATA:

Complete this section if you have recombination data for visible
markers (mutations) linked to your mutant locus.

Map location:

Note here the estimated location (in cM) of your mutant locus on
the classical genetic map.  If you have localized your gene only
to a chromosome region, use TOP, MID, or BOT.  Enter HELP if you
have recombination data but are not sure whether your gene is
ready to be placed on the genetic map.

Linked marker:

Enter here the most closely linked visible marker (already on the
classical map) for which you have recombination data.

Recombination percent:

Enter here the recombination percent (not cM) observed between
your locus and the linked marker noted above.  If your locus has
been localized between two linked markers but the precise distance
between those two markers has not been determined, enter both
markers in the previous line and leave this line blank.  Both
markers should already be on the map.

Above/below:

Enter "Above" if your mutant locus is located above (north of) the
linked marker listed on this survey.  Enter "Below" if your locus
is located below (south of) the linked marker.  Leave this line
blank if the orientation relative to the linked marker is unknown.

MOLECULAR MAP DATA:

Complete this section if you have recombination data for a linked
molecular marker included on the updated RI map available at:
http://nasc.nott.ac.uk/new_ri_map.html.  Please check this map to
confirm that your molecular marker is included.  Recombination
data for molecular markers not on the RI map cannot be used to
place genes on the classical map.

To complete this part of the form, follow the same procedure as
for the previous section, replacing visible markers with molecular
markers and classical map with RI map.

PHYSICAL MAP DATA:

In some cases, a mutant locus may correspond to a cloned gene that
has been placed on the physical map of overlapping YAC/BAC clones.
Or the mutant locus may have been mapped relative to a molecular
marker (e.g. YAC end sequence) included on the physical map but
not yet placed on the RI map.  The location of such a mutant locus
can still be estimated on the classical map by completing this
section of the form.

Anchored clone:

Enter here the type and identification number of the genomic clone
(YAC/BAC/P1/COSMID) known to contain the mutant locus.  Leave this
section blank if that clone has not been anchored to a known
location on the physical map.

Linked marker:

Enter here the most closely linked molecular marker that is also
included on the RI map.

Estimated distance:

Enter here the estimate distance (in Kb) between your mutant locus
and the molecular marker anchored on the RI and physical maps.

Orientation:

Enter here the orientation of your mutant locus relative to the
anchored molecular marker (compare with other markers on the RI
map or note whether north/south).
_________________________________________________________________

SECTION # 4:

Please use this section to make any additional comments or
corrections concerning the existing linkage table and classical
genetic map.
_________________________________________________________________





_________________________________________________________________


Regards,

David Meinke
Curator

-----
David W. Meinke
Department of Botany
Oklahoma State University
Stillwater, OK  74078
Phone: 405-744-6549
FAX:   405-744-7074 (Note change)
Email: meinke at osuunx.ucc.okstate.edu
WWW:   http://mutant.lse.okstate.edu/








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