RI map update - SNPs / SSLPs - 400+ new & updated markers

Sean May [NASC] sean_may at thale.life.nottingham.ac.uk
Tue Feb 8 11:40:37 EST 2000

We are pleased to announce that there have recently been some substantial
updates to the RI mapping data for the Lister and Dean Columbia/Landsberg

Since our last announcement regarding the RI mapping data, 1999 has seen the
incorporation of two large bulk submissions of data into the map at:
http://nasc.nott.ac.uk/new_ri_map.html .

The first  (incorporated into the June 1999 major run of Mapmaker) was
donated by Patrick Dunn pdunn at neomorph.bio.upenn.edu and Joe Ecker
jecker at atgenome.bio.upenn.edu.

This Dunn & Ecker donation includes the SSLP markers described at:
http://genome.bio.upenn.edu/SSLP_info/SSLPsordered.html .

Each primer pair amplifies a unique segment of genomic DNA containing a
simple tandem repeat. The PCR products differ in length between Columbia and
Landsberg erecta, and therefore provided the raw data for an RI analysis on
the Lister and Dean population.

Some of this data provided new markers, whereas some increased the score
densities for existing loci - where the scores were updated; all donors are
referenced in the search results.

Michael Mindrinos mindrin at sequence.stanford.edu donated a large number of
SNP (simple/single nucleotide polymorphisms) and INDEL (insertion/deletion)
RI data as reported in Cho et al.(1999) Nature Genetics 23(2):203-7. These
markers with a small number of exceptions have now been updated into the
February 2000 release of the RI map.

To avoid confusion with other large groups of SNP data that are currently
becoming available to the arabidopsis community, these markers have been
renamed at the instigation of TAIR (in agreement with Michael Mindrinos).
They are therefore represented on the map as the SGCSNP loci (Stanford
Genome Center SNPs).

All of the identifying numbers were, and are, co-linear and have been
( e.g SNP308 => SGCSNP308; and INDEL355 => SGCSNP355 )

All of the markers have also been aliased, so that searching can identify
them from EITHER the paper published codes OR the web published codes. The
search page shows both the SGC name and the original name.

Other changes to the Mapping Service for your convenience include the

* Searching for loci is now NOT case sensitive - for easier recall of locus
* Stock AND donor names are now provided in the submission form, as are
C/L/H tags for easier tracking of input by the user.
* The data submission page has been simplified.

Some of these changes were provided in response to user feedback - Thank you
for your comments, these are always welcome in regard to any aspect of NASC
/ AGR.

Sean May (NASC)

Sean_May at nasc.nott.ac.uk
Director, Nottingham Arabidopsis Stock Centre (NASC)
University Park, Nottingham University. U.K. NG7 2RD.
FON: +44 (0)115 9513237
FAX: +44 (0)115 9513297
Catalogue: http://nasc.nott.ac.uk
Genome Databases: http://synteny.nott.ac.uk
RI-maps: http://nasc.nott.ac.uk/new_ri_map.html


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