Contribution of Transposable Elements to Structural Variation and Phenotypic Adaptation in Tomato
Résumé
Structural variation has fueled phenotypic diversification and underlies important domestication and quantitative traits in crops plants. Nevertheless, the genetic drivers of plant structural variation at the population level remain poorly understood. We recently reported long-read sequencing of 100 diverse tomato genomes, which captured the extent and genomic features of structural variants. Most of this structural variation can be traced to transposable element (TE) activity. Annotation of TEs in 14 diverse accessions revealed their prevalence in tomato genomes, with a large fraction retaining transpositional potency, likely facilitating new structural variation. The Copia-like Rider family is over-represented within the TEs involved in structural variation and has generated structural variants underlying several traits of agricultural interest in tomato. Nevertheless, mechanisms regulating Rider activity remain unexplored. Through experimentally-controlled activation of the Rider family, we identified DNA methylation, phytohormones, and drought stress as molecular regulators of Rider activity in tomato. We further show differences in Rider distribution between Solanaceae species, suggesting contrasted evolutionary success of Rider and variable contribution to structural variation between species. Artificially promoting TE activity could generate agriculturally-relevant structural and epigenetic variation in tomato and related crops.