title: Transposon-based tagging: IRAP, REMAP, and iPBS.
abstract: Retrotransposons are a major component of virtually all eukaryotic genomes, which makes them useful as molecular markers. 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. To detect polymorphisms for retrotransposon insertions, marker systems generally rely on PCR amplification between the retrotransposon termini and some component of flanking genomic DNA. The main methods of IRAP, REMAP, RBIP, and SSAP all detect the polymorphic sites at which the retrotransposon DNA is integrated into the genome. Marker systems exploiting these methods can be easily developed and are inexpensively deployed in the absence of extensive genome sequence data. Here, we describe protocols for the IRAP, REMAP, and iPBS techniques, including methods for PCR amplification with a single primer or with two primers, and agarose gel electrophoresis of the product using optimal electrophoresis buffers; we also describe iPBS techniques for the rapid isolation of retrotransposon termini and full-length elements.
authors.affiliation: MTT/BI Plant Genomics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Ruslan
authors.initials: R
authors.lastname: Kalendar
authors.forename: Alan H
authors.initials: AH
authors.lastname: Schulman
mesh_terms: D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D004262:DNA Restriction Enzymes / Q000378:metabolism; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D018895:Microsatellite Repeats / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D018626:Retroelements / Q000235:genetics*
chemical_list: D017931:DNA Primers; D018744:DNA, Plant; D018626:Retroelements; D004262:DNA Restriction Enzymes