Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis

Authors

  • Andrew J. Flavell,

    1. 1 Department of Biochemistry, University of Dundee, MSI/WTB Complex, Dow Street, Dundee DD1 5EH, UK, and 2 John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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  • 1 , Maggie R. Knox,

    1. 1 Department of Biochemistry, University of Dundee, MSI/WTB Complex, Dow Street, Dundee DD1 5EH, UK, and 2 John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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  • 2 Stephen R. Pearce,

    1. 1 Department of Biochemistry, University of Dundee, MSI/WTB Complex, Dow Street, Dundee DD1 5EH, UK, and 2 John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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  • and 1 T. H. Noel Ellis 2

    1. 1 Department of Biochemistry, University of Dundee, MSI/WTB Complex, Dow Street, Dundee DD1 5EH, UK, and 2 John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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*For correspondence (fax +44 1382 322558/201063; e-mail a.j.flavell@dundee.ac.uk).

Summary

Two assays based upon PCR detection of a polymorphic PDR1 retrotransposon insertion in Pisum sativum have been developed. Both methods involve PCR with primers derived from the transposon and flanking DNA. The first method uses a dot assay for PCR product detection which could be fully automated for handling thousands of samples. The second method, which is designed to handle lower numbers, requires a single PCR and gel lane per sample. Both methods yield co-dominant markers, with presence and absence of the transposon insertion independently scorable, and both could in principle be applied to any transposable element in any plant species.

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