Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry

Transposable elements (TEs) constitute a major portion of plant genomes and play key roles in shaping genome architecture, regulating gene expression, and driving genome evolution. In this study, we generated a comprehensive and curated TE library for the woodland strawberry ( Fragaria vesca ) by integrating two bioinformatic pipelines (EDTA and DeepTE). Our annotation revealed that TEs account for approximately 37% of the F. vesca genome. Analysis of TE-derived inverted repeats (IRs) and miniature inverted-repeat transposable elements (MITEs) demonstrated their association with 24-nt small interfering RNA (siRNA) production and differential DNA methylation patterns across tissues, suggesting a role in the epigenetic regulation of gene expression, particularly during fruit ripening. This MITE-mediated epigenetic regulatory mechanism was confirmed by evaluating gene expression and chromatin organization at FvH4_7g18570, which encodes the alcohol acyl transferase ( FvAAT1 ). Three MITEs located upstream or downstream of the FvAAT1 coding sequence were shown to influence epigenetically this gene expression. Furthermore, we analyzed 210 re-sequenced accessions from the F. vesca European germplasm collection to identify and annotate TE insertion and deletion polymorphisms. A principal component analysis (PCA) based on these polymorphisms revealed subpopulation structures that reflect geographic origins. A genome-wide association study (GWAS) uncovered significant associations between specific TE polymorphisms and economically important fruit traits, including aroma-related volatile compounds and fruit size. Among them, the insertion of a hAT MITE near FvH4_2g00610 correlated with increased levels of γ-decalactone, a desirable aroma compound in strawberries. These findings underscore the functional significance of TE-derived elements as key contributors to phenotypic diversity through novel regulatory functions. By integrating TE polymorphisms into population-genomic and functional studies, this work provides valuable insights into strawberry fruit development and quality traits. It also highlights the potential of harnessing TE-mediated variation in breeding initiatives and genome editing strategies to improve fruit quality.