title: The application of LTR retrotransposons as molecular markers in plants.
abstract: Retrotransposons are major, dispersed components of most eukaryotic genomes. They replicate by a cycle of transcription, reverse transcription, and integration of new copies, without excising from the genome in the process. Because they represent a major share of the genome, cause easily detectable genetic changes having known ancestral and derived states, and contain conserved regions for which polymerase chain reaction (PCR) primers may be designed, retrotransposon insertions can be exploited as powerful molecular marker systems. Here, we describe the background and strategies, as well as give detailed laboratory protocols, for four key retrotransposon-based methods: SSAP, IRAP, REMAP, and RBIP. The SSAP, IRAP, and REMAP methods are multiplex and generate anonymous marker bands; RBIP scores individual loci, much as microsatellite-based marker systems do. The methods are variously suited to marker detection on agarose and polyacrylamide slab gels, slab and capillary sequencing devices, and arrays on solid supports. The different strengths and weaknesses of these approaches and their performance relative to conventional marker methods are discussed, together with their applicability to marker-assisted breeding, phylogenetic analyses, biodiversity determinations, and evolutionary studies.
authors.affiliation: MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Finland.
authors.forename: Alan H
authors.initials: AH
authors.lastname: Schulman
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Flavell
authors.forename: T H Noel
authors.initials: TH
authors.lastname: Ellis
mesh_terms: D015415:Biomarkers; D018744:DNA, Plant / Q000032:analysis*; D004268:DNA-Binding Proteins / Q000032:analysis; D002523:Edible Grain / Q000235:genetics*; D018532:Pisum sativum / Q000235:genetics*; D010940:Plant Proteins / Q000032:analysis; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D019105:Random Amplified Polymorphic DNA Technique; D018626:Retroelements / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins; D020079:Terminal Repeat Sequences / Q000235:genetics*; D015534:Trans-Activators / Q000032:analysis; D014157:Transcription Factors; D016335:Zinc Fingers
chemical_list: C082800:BARE-1 protein, Hordeum vulgare; D015415:Biomarkers; D018744:DNA, Plant; D004268:DNA-Binding Proteins; C085480:PDR1 protein, S cerevisiae; D010940:Plant Proteins; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors