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Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome

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Abstract

Four previously undescribed families of miniature inverted repeat transposable elements (MITEs) were isolated by searching barley genomic DNA using structure-based criteria. Putative MITEs were confirmed by PCR to determine their insertional polymorphism in a panel of diverse barley germplasm. Copy numbers for all these familes are somewhat low (less than 1,000 copies per family per haploid genome). In contrast to previous studies, a higher proportion of insertions of the new MITEs are found within known transposable elements (27%) than are associated with genes (15%). Preliminary studies were conducted on two of the new MITE families to test their utility as molecular markers. Insertional polymorphism levels for both the families are high and diversity trees produced by both the families are similar and congruent with known relationships among the germplasm studied, suggesting that both the MITE families are useful markers of barley genetic diversity.

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Abbreviations

MITE:

Miniature inverted repeat transposable element

TE:

Transposable element

SSAP:

Sequence-specific amplification polymorphisms

IRAP:

Inter-repeat amplification polymorphisms

TIR:

Terminal inverted repeat

TSD:

Terminal sequence duplication

AFLP:

Amplified fragment length polymorphism

BAC:

Bacterial artificial chromosome

TBE:

TRIS–borate–EDTA

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Acknowledgments

We are grateful to Ali Massoudi, Luke Ramsay, Katie Caldwell and Tim Close for supplying unpublished barley DNA sequence for this study and Alan Schulman for helpful comments. This work was financially supported by a BBSRC PhD studentship to ML. We are also grateful for technical support and advice from Sharon Mudie.

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Author notes

  1. Nils Rostoks

    Present address: Faculty of Biology, University of Latvia, 4 Kronvalda Boulevard, Riga, 1586, Latvia

Authors and Affiliations

  1. Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee, DD2 5DA, UK

    Maura Lyons, Robbie Waugh & Andrew J. Flavell

  2. Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    Linda Cardle & Nils Rostoks

Authors
  1. Maura Lyons
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  2. Linda Cardle
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  4. Robbie Waugh
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Corresponding author

Correspondence to Andrew J. Flavell.

Additional information

Communicated by M.-A. Grandbastien.

Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. EU822304–EU822308.

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Lyons, M., Cardle, L., Rostoks, N. et al. Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome. Mol Genet Genomics 280, 275–285 (2008). https://doi.org/10.1007/s00438-008-0363-0

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  • DOI: https://doi.org/10.1007/s00438-008-0363-0

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