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

Adnane Nemri; Michael M Neff; Michael Burrell; Jonathan D.G Jones; David J Studholme

doi:10.1093/bioinformatics/btm501

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

Journal article

Open access

Peer reviewed

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

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

Bioinformatics, Vol.23(22), pp.3108-3109

11/15/2007

DOI: https://doi.org/10.1093/bioinformatics/btm501

Handle:

https://hdl.handle.net/2376/110114

PMID: 18025007

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Abstract

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

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Title: Marker development for the genetic study of natural variation in Arabidopsis thaliana
Creators: Adnane Nemri - 1Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
Michael M Neff - 1Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
Michael Burrell - 1Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
Jonathan D.G Jones - 1Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
David J Studholme - 1Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
Publication Details: Bioinformatics, Vol.23(22), pp.3108-3109
Academic Unit: Crop and Soil Sciences, Department of
Publisher: Oxford University Press
Identifiers: 99900547478901842
Language: English
Resource Type: Journal article