Molecular Genetics and Genomics

, Volume 280, Issue 4, pp 275–285

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

DOI: 10.1007/s00438-008-0363-0

Cite this article as:
Lyons, M., Cardle, L., Rostoks, N. et al. Mol Genet Genomics (2008) 280: 275. doi:10.1007/s00438-008-0363-0

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.

Keywords

BarleyGenetic diversityTransposable elementSSAPMITE

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

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)

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