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The application of LTR retrotransposons as molecular markers in plants

The application of LTR retrotransposons as molecular markers in plants

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

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  • Alan H. Schulman
  • Alan J. Flavell
  • Etienne Paux
  • T. H. Noel Ellis


Original languageEnglish
Title of host publicationMobile genetic elements
Subtitle of host publicationprotocols and genomic applications
EditorsJohn M. Walker, Yves Bigot
Place of PublicationNew York
PublisherHumana Press
Number of pages39
ISBN (Electronic)9781617796036
ISBN (Print)9781617796029
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
PublisherHumana Press
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction.

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