PT  - JOURNAL ARTICLE
AU  - Marisol Domínguez
AU  - Elise Dugas
AU  - Médine Benchouaia
AU  - Basile Leduque
AU  - José Jimenez-Gomez
AU  - Vincent Colot
AU  - Leandro Quadrana
TI  - The impact of transposable elements on tomato diversity
AID  - 10.1101/2020.06.04.133835
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.04.133835
4099  - http://biorxiv.org/content/early/2020/06/04/2020.06.04.133835.short
4100  - http://biorxiv.org/content/early/2020/06/04/2020.06.04.133835.full
AB  - Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.Competing Interest StatementThe authors have declared no competing interest.