[Arabidopsis] a database for markers between ecotypes

Norman Warthmann norman at warthmann.com
Tue Nov 22 07:32:12 EST 2005


Dear all,

This is in response to the post of Xiaodong Sun (Nov 8th), who  
apparently is looking for molecular markers between the ecotypes WS  
and Ler.
We had the problem of marker mining between ecotypes frequently in  
the past and decided to setup a database for collecting and  
retrieving polymorphism data. Its brand new, not yet published and  
preliminarily available at

http://www.eb.tuebingen.mpg.de/msqt/	( do not drop the trailing "/")

The only data currently uploaded was parsed from a dataset from  
Magnus Nordborg, USC; this is >1200 sequenced PCR fragments from 98  
ecotypes and was downloaded from http://walnut.usc.edu/2010; most of  
this data is published.

Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, et al. (2005)
The Pattern of Polymorphism in Arabidopsis thaliana. PLoS Biol 3(7):  
e196

The usage should be clear after reading the documentation/FAQ. You  
are welcome to use the tool and we hope it is useful to you. In that  
case we ask you to cite the Nordborg paper and acknowledge us. Our  
own publication is in preparation.

However, there is no warranty whatsoever; so please confirm the  
polymorphisms yourself before spending big bucks on SNP-assays!

regards

Norman

----
Norman Warthmann
Max-Planck-Institute for Developmental Biology
Dept. Molecular Biology
http://www.smartgradstudent.de



------------------------------

Message: 2
Date: Tue, 08 Nov 2005 11:25:50 CST
From: Xiaodong Sun <sunxx114 at umn.edu>
Subject: [Arabidopsis] Request for polymorphism markers on WS x Ler
To: arab-gen at magpie.bio.indiana.edu
Message-ID: <200511081725.jA8HPoMP022161 at barricade.software.umn.edu>
Content-Type: TEXT/plain; CHARSET=US-ASCII

Dear all,

I would like to request for molecular markers for mapping on WS x Ler
background.
I am working on positional cloning. The mutants I have are based on WS
background, so most of our markers from Col x Ler background didn't  
work at
all. If anyone have reliable markers for rough mapping on WS x Ler
background, would you please send me the sequences? I especially need  
the
markers on Chromosome 4, but on other Chs is also helpful.

Many thanks

Sincerely,
Xiaodong Sun
Plant Biological Science Graduate Program
University of Minnesota, Twin cities




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