CAPS/SSLP markers on chr1

Sue Rhee rhee at acoma.Stanford.EDU
Thu Dec 16 21:08:08 EST 1999


Dear Suk-Hwan,

You can find markers that hybridize, or match by sequence, to AGI clones
on TAIR's Sequence Map or Sequence Table.

The following are markers that lie between ATPase (ATHATPase) and the
southern end of the chromosome on our Seq Map and Seq Table:

SGCSNP231
nga692--PCR
ADH--PCR
nF22K20--PCR
ve011
SGCSNP253
g17311
SGCSNP142
mi157
SGCSNP355

In addition, there are also four AT simple repeats between these two
sites, in our Seq Table, which may be candidates for SSLP markers.

Some of these SGCSNPs (Stanford Genome Center SNPs) may have a restriction
enzyme site at the polymorphic site, which then can be turned into a CAPS
marker.

I've used our Restrction Analysis Program to find any polymorphic sites
for the above SGCSNPs and found that three out of the four SNPs have a
restriction site polymorphism! You would need to design primers to regions
that flank these SNPs to make CAPs markers out of these. The nucleotide
position of these SNPs within an AGI clone and a link to the clone's
sequence are provided in our Sequence Table.

SGCSNP231: XmnI cuts in Ler, does not cut in Col
SGCSNP253: ClaI cuts in Col, does not cut in Ler
SGCSNP142: SspI cuts in Ler, does not cut in Col
SGCSNP355: Sorry, no restriction polymporphsim here.

The following URLs denote the tools and data I've mentioned above:

TAIR Homepage: 	http://arabidopsis.org
Sequence Map:	http://arabidopsis.org/cgi-bin/maps/Schrom
Sequence Table:	http://arabidopsis.org/cgi-bin/maps/Seqtable.pl
SNP Table:	http://arabidopsis.org/SNPs.html
Restriction Analysis:

	http://arabidopsis.org/cgi-bin/patmatch/RestrictionMapper.pl

If you end up making markers from these SNPs or dinucleotide repeats, we
would love to include that information in our Marker list we are currently
building. Please let us know.

Cheers,
Sue

On Mon, 13 Dec 1999, Elizabeth Vierling wrote:

> Dear colleagues,
> We have been working in the region on chromosome 1 between SSLP marker
> ATHATPase and the bottom of chromosome1. Does anyone have information on
> additional PCR based markers in this region? It would be greatly
> helpful.
>
> Thanks in advance for your help,
>
> Suk-Whan Hong.
> Biochemistry Department
> University of Arizona
> Life Sciences South
> 1007 E. Lowell St.
> Tucson, Arizona  85721
> USA
>
> Phone: 520-621-3977
> Fax: 520-621-3709
>
> E-mail: sukwhan at u.arizona.edu
>
>
>
>

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-------------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
					FAX: +1-650-325-6857
Carnegie Institution of Washington	Tel: +1-650-325-1521 ext. 251
Department of Plant Biology
260 Panama St.
Stanford, CA 94305
U.S.A.
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