How important are transposons for plant evolution?

Key Points Transposable elements (TEs) are the single most variable components of plant genomes. Even closely related plants can harbour widely different populations of TEs. TEs can cause a broad array of changes in gene composition and function. These changes range from simple insertional mutations to genetic reprogramming, gene movement and the evolution of novel functional protein-coding sequences. To restrain TE activity, plants have a potent response that results in epigenetic silencing of these elements. This can in turn result in epigenetic as well as genetic variation in plant gene function. The changes caused by TEs are a potentially rich source of variation on which selection can operate. Given the large numbers of plant TEs on evidence for ongoing activity of these selfish genetic elements, it is a reasonable hypothesis that TEs have played an important part in plant adaptation. Despite the possibilities raised by experimental evidence of the kinds of changes that TEs can cause, there is only limited and anecdotal evidence that TEs have in fact been important players in adaptive evolution of plants. Recent advances in genomics and phenomics have made it possible systematically to assess the part that TEs have played. It is only through the systematic identification of large numbers of alleles with important effects on phenotype that it will be possible to determine the relative role that TEs have had in the generation of meaningful genetic variation in plants. Domesticated plant species provide us with an ideal model for understanding this process. These species have been under strong, recent directional selection, often have well-characterized TEs, have been extensively characterized with respect to trait variation and can be readily compared to wild relatives. Transposable elements are important sources of genetic and epigenetic variation in plant genomes. The author discusses the evidence that this variation has been important for plant evolution and how new genomic resources should allow a systematic assessment of this issue. For decades, transposable elements have been known to produce a wide variety of changes in plant gene expression and function. This has led to the idea that transposable element activity has played a key part in adaptive plant evolution. This Review describes the kinds of changes that transposable elements can cause, discusses evidence that those changes have contributed to plant evolution and suggests future strategies