Plant transposable elements: where genetics meets genomics

The analysis of unstable kernel phenotypes in maize led to the discovery and characterization of active class 2 DNA transposable elements (TEs). These active elements are a very small fraction of the TEs found in plant genomes. Access to all or part of the genomic sequence of an organism has led to the development of new techniques to analyse the life cycle of TEs and their interactions with the 'host' genome. Two types of element — miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons — predominate in plant genomes. MITEs are non-autonomous class 2 elements, but most can now be connected with two superfamilies of transposases: Tc1/mariner and PIF/harbinger. LTR retrotransposons are the single largest component of plant genomes and are responsible for the recent genome expansion in some plants. Despite evidence of recent activity, TEs that are present in high copy numbers in plant genomes are almost universally found to be defective and/or epigenetically silenced. Some LTR retrotransposons are transcriptionally activated by various biotic and abiotic stresses. Availability of mutant backgrounds that are deficient in epigenetic regulation offers the promise of activating previously silenced TEs and revealing new facets of their biology.