Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome
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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.
KeywordsBarley Genetic diversity Transposable element SSAP MITE
Miniature inverted repeat 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We are grateful to Ali Massoudi, Luke Ramsay, Katie Caldwell and Tim Close for supplying unpublished barley DNA sequence for this study and Alan Schulman for helpful comments.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.
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