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iPBS: a universal method for DNA fingerprinting and retrotransposon isolation

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Abstract

Molecular markers are essential in plant and animal breeding and biodiversity applications, in human forensics, and for map-based cloning of genes. The long terminal repeat (LTR) retrotransposons are well suited as molecular markers. As dispersed and ubiquitous transposable elements, their “copy and paste” life cycle of replicative transposition leads to new genome insertions without excision of the original element. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Nevertheless, up to a year has been required to develop a retrotransposon marker system in a new species, involving cloning and sequencing steps as well as the development of custom primers. Here, we describe a novel PCR-based method useful both as a marker system in its own right and for the rapid isolation of retrotransposon termini and full-length elements, making it ideal for “orphan crops” and other species with underdeveloped marker systems. The method, iPBS amplification, is based on the virtually universal presence of a tRNA complement as a reverse transcriptase primer binding site (PBS) in LTR retrotransposons. The method differs from earlier retrotransposon isolation methods because it is applicable not only to endogenous retroviruses and retroviruses, but also to both Gypsy and Copia LTR retrotransposons, as well as to non-autonomous LARD and TRIM elements, throughout the plant kingdom and to animals. Furthermore, the inter-PBS amplification technique as such has proved to be a powerful DNA fingerprinting technology without the need for prior sequence knowledge.

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Abbreviations

LTR:

Long terminal repeat

PBS:

Primer binding site

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Acknowledgments

We thank the many collaborators listed in Online Resource 1 for gifts of plant materials. Eeva-Marja Turkki, Anne-Mari Narvanto, and Ursula Lönnqvist are thanked for their always excellent technical assistance. The work was supported by Ministry of Education of Czech Republic project MSM2678424601 and by the Academy of Finland, Grant 120810, Project Exbardiv of the ERA-NET Plant Genomics program.

Author information

Authors and Affiliations

  1. MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 65, Helsinki, Finland

    Ruslan Kalendar & Alan H. Schulman

  2. Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland

    Kristiina Antonius & Alan H. Schulman

  3. Department of Plant Biotechnology, Agritec Plant Research Ltd., Zemědělská 2520/16, 787 01, Šumperk, Czech Republic

    Petr Smýkal

Authors
  1. Ruslan Kalendar
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  2. Kristiina Antonius
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  3. Petr Smýkal
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  4. Alan H. Schulman
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Corresponding author

Correspondence to Alan H. Schulman.

Additional information

Communicated by T. Komatsuda.

Accession numbers for the sequences resulting from this study: AF538603, AF538607–AF538610, AF538612–AF538617, AJ489246, AY078073–AY078075AY271961, AY643843, AY860307, AY860308, DQ094839–DQ094843, DQ663704–DQ663717, EF19100, EF191001, EF191002, EF191007, EF191008, EF191009, EF191011, EF191012, EF439837, EF555576–EF555582, EU009616–EU009622, EU009624, EU090224, EU105454–EU105459, EU177767–EU177770, EU180578, EU180581–EU180586.

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Online Resource 1 (PDF 91 kb)

Online Resource 2 (PDF 1,236 kb)

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Kalendar, R., Antonius, K., Smýkal, P. et al. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121, 1419–1430 (2010). https://doi.org/10.1007/s00122-010-1398-2

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