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Bioinformatics 2007 23(22):3108-3109; doi:10.1093/bioinformatics/btm501
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Marker development for the genetic study of natural variation in Arabidopsis thaliana

Adnane Nemri 1,*, Michael M. Neff 2, Michael Burrell 1, Jonathan D.G. Jones 1 and David J. Studholme 1

1Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA

*To whom correspondence should be addressed.


  Abstract

Summary: We report AtPRIMER, an application that automates the discovery of new polymorphic markers between ecotypes of Arabidopsis thaliana. On specifying two ecotypes and the genomic region of interest, the script retrieves all corresponding single nucleotide polymorphisms (SNPs) and generates CAPS and/or dCAPS PCR primer sequences. We show that AtPRIMER accurately found specific polymorphic markers for our linkage mapping project. AtPRIMER will therefore be useful for efficient marker development with high density and specificity.

Availability: This PERL/CGI program is available for non-commercial users at http://www.AtPRIMER.tsl.ac.uk. The web-based version is available for public use at the same URL.

Contact: adnane.nemri@tsl.ac.uk

Associate Editor: Martin Bishop

Received on August 8, 2007; revised on September 28, 2007; accepted on September 28, 2007

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