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Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity

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Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2222))

Abstract

Retrotransposable elements (RTEs) are highly common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The “copy-out and paste-in” life cycle of replicative transposition in these dispersive and ubiquitous RTEs leads to new genome insertions without excision of the original element. RTEs are important drivers of species diversity; they exhibit great variety in structure, size, and mechanisms of transposition, making them important putative components in genome evolution. Accordingly, various applications have been developed to explore the polymorphisms in RTE insertion patterns. These applications include conventional or anchored polymerase chain reaction (PCR) and quantitative or digital PCR with primers designed for the 5′ or 3′ junction. Marker systems exploiting these PCR methods can be easily developed and are inexpensively used in the absence of extensive genome sequence data. The main inter-repeat amplification polymorphism techniques include inter-retrotransposon amplified polymorphism (IRAP), retrotransposon microsatellite amplified polymorphism (REMAP), and Inter-Primer Binding Site (iPBS) for PCR amplification with a single or two primers.

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Acknowledgments

This work was partially supported by the Government of Perm Krai, research project no. С-26/174.3 on January 31, 2019.

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Authors and Affiliations

  1. Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, Helsinki, Finland

    Ruslan Kalendar

  2. National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan

    Ruslan Kalendar

  3. The Federal Research Center Institute of Cytology and Genetics, Novosibirsk, Russian Federation

    Alexander Muterko

  4. Department of Botany and Genetics of Plants, Faculty of Biology, Perm State University, Perm, Russia

    Svetlana Boronnikova

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  1. Ruslan Kalendar
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  2. Alexander Muterko
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Correspondence to Ruslan Kalendar .

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  1. UMR PVBMT, Universite de la Reunion, St Pierre, Réunion, France

    Pascale Besse

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Kalendar, R., Muterko, A., Boronnikova, S. (2021). Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 2222. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0997-2_15

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