Arabidopsis Sha Vs.Tsu-1 markers

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Arabidopsis Sha Vs.Tsu-1 markers

gat kr
Hi all,
I was wondering if anyone knows a good, reliable PCR based marker to
distinguish between Sha and Tsu-1.
Alternatively, does anybody know of a web based SNP tool that has these 2
ecotypes in its database?
Thanx,
Gat
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Re: Arabidopsis Sha Vs.Tsu-1 markers

Olivier Loudet-2
   Hi,
You may want to use the ANATool website for that purpose
https://www.versailles.inra.fr/ijpb/crb/anatool/
which contains genotypes for 341 SNP markers x 591 accessions (including
Sha and Tsu-1) and tools to interrogate this dataset in different useful
ways. For example you can find the minimal marker set to discriminate
between 2 or more accessions, or the minimal fingerprint of one accession
(within this matrix).
This is based on Simon et al., Plant J., 2012:
http://www.ncbi.nlm.nih.gov/pubmed/22077701
PDF:
http://www.inra.fr/vast/Files/Simon_PlantJournal_2011.pdf

Depending on your exact goal, of course Sha and Tsu-1 are also included
among the 1001 accessions currently being sequenced:
http://www.1001genomes.org/

PS: In any case, always double-check the genotypes of accessions on your
seed lot, as there will always be (at least) punctual differences between
different SSDs.

O.


Le 04/09/2012    10:09,gat kr √©crit:

>Hi all,
>I was wondering if anyone knows a good, reliable PCR based marker to
>distinguish between Sha and Tsu-1.
>Alternatively, does anybody know of a web based SNP tool that has these 2
>ecotypes in its database?
>Thanx,
>Gat
>_______________________________________________
>Arab-gen mailing list
>[hidden email]
>http://www.bio.net/biomail/listinfo/arab-gen

O.
________________________________________________________

             Olivier Loudet

   INRA, National Institute for Agricultural Research
   IJPB, Versailles, France

  V.A.S.T group -- Variation and Abiotic Stress Tolerance

      Mail: [hidden email]
      Science: www.inra.fr/vast

   " Catch your Fire in your Turn and Let it Burn "
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