Linkage Data Summary for Visible Markers

Mike Cherry 726-5955 CHERRY at FRODO.MGH.HARVARD.EDU
Wed Dec 30 10:53:36 EST 1992


[
Note: A printed copy of the following table, created by David Meinke,
was included in the recent postal mailing from the ABRC at Ohio State.
This table is now electronically available from the Arabidposis
Research Companion Gopher in the "Arabidopsis Genetic Maps and Tables"
folder. The information contained within this table has been
incorporated into the AAtDB database available via gopher and wais.
The next version of the Unix AAtDB database, release 1-4, will also
contain this information.

Special thanks go to David Meinke for volunteering to be the Genetics
Curator for Arabidopsis.

Mike Cherry
AAtDB Project
]


      Linkage Data - Mutant Gene Markers of Arabidopsis thaliana
				   
		 Explanation of Attached Information
				   
		      David W. Meinke (12/15/92)

The attached information summarizes existing linkage data for mutant
genes of Arabidopsis thaliana.  Information on molecular markers and
cloned wild- type genes is not included.  This table was constructed
in response to the mapping survey recently distributed to the
Arabidopsis community.  The main purpose of this table is to summarize
information on linked visible markers and approximate map locations
for mutant genes.  Over 260 genetic loci are included in this table.

Contributors will be asked in the future to submit recombination data
in a standardized format to facilitate construction of updated maps.
Forms and additional information will be distributed to the
Arabidopsis community in the near future.

Please send additions and/or corrections to this linkage table to:
David Meinke, curator: FAX 405-744-7673; phone 405-744-6549; email:
btnydwm at osucc.bitnet; or to Mike Cherry
(curator at frodo.mgh.harvard.edu).

Additional information on each column of this table is presented
below.

Mutant Locus: This lists each mutant locus for which recombination
data are available.  I have added a space between the gene symbol and
locus number to avoid confusion between the letter "l" and the number
"1".

Linkage Group: (Self-explanatory)

Map:  This reveals the current status of the locus with respect to mapping.

      M: The mutant locus is included on the attached visible marker
         map.
      R: The mutant locus should be ready to add to the visible marker
         map once recombination data are obtained in the appropriate
         format.
      X: The mutant locus is not ready to place on the map, often
         because recombination data are available for only a single
         linked marker.
      U: The precise status of this locus with respect to placement on
         the map is currently unresolved.

Closest Marker Tested: This shows the most closely-linked visible
marker (already on the map) for which recombination data with the
mutant locus in question are available.  Other visible markers may be
more closely linked, but recombination data with those markers have
not been reported.  In some cases, no recombinants were found among
relatively small populations of F2 plants.  Recombination estimates
(0.00) for these markers were frequently misleading and inconsistent
with data for other closely-linked markers.  Information on additional
linked markers has therefore been included for these mutants.
Molecular markers are included in this column only if recombination
data for linked visible markers are not available.

r: This shows the recombination estimate (%) between the mutant locus
in column #1 and the most closely-linked marker tested in column #4.
A/B: This summarizes what is known about the relative orientation of
the mutant locus and linked marker.

      A: The mutant locus in column 1 has been definitively shown to
         be Above the marker on the genetic map.  This fixed order has
         also been given to JOINMAP.

      B: The mutant locus in column 1 has been definitively shown to
         be Below the marker on the genetic map.  This fixed order has
         also been given to JOINMAP.

      *: The fixed order noted above is not reflected on the current
         map because it is somewhat inconsistent with other 2-point
         data and was consequently rejected by JOINMAP.  Efforts are
         underway to resolve the inconsistencies associated with these
         fixed orders.

      a: If the mutant locus is on the map, then JOINMAP has placed
         this locus above the closest tested marker shown in column 4,
         though this location has not been confirmed.  In the
         remaining cases, other data indicate that the mutant locus is
         above the marker.

      b: Same as described above for "a", but in this case, the mutant
         locus is below the tested marker.
             
LOD: This calculation performed by JOINMAP illustrates the certainty
of tight linkage between the mutant locus and tested marker.  A high
LOD score indicates a high degree of certainty of tight linkage
between the two genes.  High LOD scores result from large F2
populations, small standard errors, and small recombination estimates.

Current Location: This shows the current estimated map location of the
mutant locus on the attached visible marker map constructed by JOINMAP
with visible marker data only.

Reference Laboratory: This lists the laboratory that contributed the
recombination data for the mutant locus and most closely-linked
visible marker.  Other laboratories may have initially placed the
mutant locus on the map or contributed additional recombination data.
This column has been left blank if the source of the corresponding
recombination data has not yet been identified.

Suggested Protocol for the Future:

Place greater emphasis on mapping the chromosomal location of your
favorite mutant gene prior to publication.

Perform complementation tests between your mutant and other
closely-linked mutants with related phenotypes.

Report preliminary linkage information for your mutant gene as soon as
possible by contacting David Meinke at 405-744-6549 (phone),
405-744-7673 (FAX), or btnydwm at osucc.bitnet (email).  Initial linkage
assignments may be reported even before the precise map location has
been determined.  Direct submission of mapping data to existing
databases is planned for the future.
				   


		   Summary of Current Linkage Data
				   
	      Mutant Gene Markers - Arabidopsis thaliana
				   
	     Updated December 15, 1992;  David W. Meinke
				   
	    See Attached Page for Explanations of Columns
				   

______________________________________________________________________________

                         Closest                   
Mutant    Linkage        Marker                        Current    Reference
Locus      Group   Map   Tested    r     A/B   LOD    Location   Laboratory
______________________________________________________________________________

aba         5      M     min       6.8    b    13.6     97.1      Koornneef
abi1        4      M     cer2      3.0    b    31.4     50.4      Koornneef
abi2        5      R     tz        -      -     -        -        Finkelstein
abi3        3      M     gl1      10.2    a   113.6     37.9      Koornneef
aca1        5      X     -         -      -     -        -        Lehle
acd1        3      R     gl1      20.7    b     -        -        Ausubel
acd2        4      X     ap2       -      -     -        -        Ausubel
act1        1      M     an       30.1    B     2.8     35.3      Somerville
adh         1      R     clv1      5.5    a     -        -        Meyerowitz
ag          4      M     ch42      2.8    a    20.6     38.1      Koornneef
alb1        1      M     ga4       0.0    A     5.6     12.1      Koornneef
                         dis1     10.4    a   145.0      -        Koornneef
alb2        5      M     co        1.2    b    50.5     15.8      Koornneef
amt1        5      X     ASA-1    <1.0    -     -        -        Town
an          1      M     emb76     0.4    B*  165.1      1.0      Meinke   
ap1         1      M     cer6      2.3    b     3.9    100.8      Koornneef
ap2         4      M     cer4      0.0    b     5.7     64.0      Koornneef
                         fad4      0.0    a     5.1      -        Somerville
                         fd        1.2    b   103.9      -        Koornneef
ap3         3      M     tt5       0.0    b    60.2     84.6      Koornneef
                         gl1      35.6    B     5.3      -        Koornneef
ara1        4      M     fca       0.2    b     -       32.5      Cobbett
as          2      M     re        0.0    b     5.1     58.2      Koornneef
                         emb18     0.6    A*  106.3      -        Meinke
aux         2      M     hy1      14.7    a     7.8     23.9      Koornneef
axr1        1      R     dis1      6.6    a     -        -        Estelle 
axr2        3      M     gl1      12.5    a    22.2     33.8      Estelle  
axr3        1      R     axr1      1.0    a     -        -        Estelle
bio1        5      M     tz        3.7    a   102.2     74.5      Meinke
bp          4      M     emb178    2.0    a    79.2      8.6      Meinke   
cad1        5      U     tt3       -      -     -        -        Cobbett
cer1        1      M     an        0.7    b    71.5      1.7      Koornneef
cer2        4      M     emb140    0.0    -   100.3     48.1      Meinke   
                         fad6      0.0    a     6.7      -        Somerville
                         ga5       1.1    a   245.6      -        Koornneef
cer3        5      M     lfy       0.0    a    11.2     82.3      __________
                         tz        5.1    b   276.7      -        Koornneef
cer4        4      M     ap2       0.0    a     5.7     57.0      Koornneef
                         ga5       0.0    b     2.4      -        Koornneef
                         cp3      14.5    a     9.4      -        Koornneef
cer5        1      M     ch1       0.0    b     5.2     71.2      Koornneef
                         clv2     16.2    a     3.8      -        Koornneef
cer6        1      M     ap1       2.3    a     3.9     97.2      Koornneef
cer7        3      M     emb78     0.4    b   165.1     90.9      Meinke   
cer8        2      M     emb39     0.3    a    97.1     70.0      Meinke   
cer9        4      M     ap2       8.6    b     8.1     72.4      Koornneef
ch1         1      M     cer5      0.0    a     5.2     59.5      Koornneef
                         emb22     3.9    a   134.4      -        Meinke
ch5         5      M    


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