Molecular Genetics and Genomics

, Volume 280, Issue 4, pp 275–285 | Cite as

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

  • Maura Lyons
  • Linda Cardle
  • Nils Rostoks
  • Robbie Waugh
  • Andrew J. Flavell
Original Paper


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.


Barley Genetic diversity Transposable element SSAP MITE 



Miniature inverted repeat transposable element


Transposable element


Sequence-specific amplification polymorphisms


Inter-repeat amplification polymorphisms


Terminal inverted repeat


Terminal sequence duplication


Amplified fragment length polymorphism


Bacterial artificial chromosome





We are grateful to Ali Massoudi, Luke Ramsay, Katie Caldwell and Tim Close for supplying unpublished barley DNA sequence for this study and Alan Schulman for helpful comments.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.

Supplementary material

438_2008_363_MOESM1_ESM.doc (98 kb)
Supplementary Fig. 1. An example of an autoradiograph from copy number screens of a barley BAC genomic clone library using Talisker overgo probe. Positive clones correspond to adjacent double spots (DOC 98 kb)
438_2008_363_MOESM2_ESM.doc (150 kb)
Supplementary Table 1: Primers used to screen for insertional polymorphism of putative MITEs (DOC 150 kb)
438_2008_363_MOESM3_ESM.doc (56 kb)
Supplementary Table 2: Primers used for SSAP analysis of MITE insertional polymorphism (DOC 56 kb)
438_2008_363_MOESM4_ESM.doc (51 kb)
Supplementary Table 3: Overgo Primers used for BAC filter screening (DOC 51 kb)
438_2008_363_MOESM5_ESM.doc (77 kb)
Supplementary Table 4. (a) Identification of grouped MITE elements, (b) Identification of singleton MITEs (DOC 77 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Maura Lyons
    • 1
  • Linda Cardle
    • 2
  • Nils Rostoks
    • 2
    • 3
  • Robbie Waugh
    • 1
  • Andrew J. Flavell
    • 1
  1. 1.Division of Plant SciencesUniversity of Dundee at SCRI, InvergowrieDundeeUK
  2. 2.Genetics Programme, Scottish Crop Research Institute, InvergowrieDundeeUK
  3. 3.Faculty of BiologyUniversity of LatviaRigaLatvia

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