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Updated: Dec 12, 2025

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
Published on: January 20, 2023
The impact of transposable elements on tomato diversity
Marisol Domínguez1, Elise Dugas1, Médine Benchouaia2
1Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France.
Transposable elements (TEs) significantly drive tomato diversity by creating numerous insertion polymorphisms (TIPs). These genetic variations impact gene expression and are linked to key agronomic traits, offering new breeding opportunities.
Area of Science:
- Plant genetics
- Genomics
- Evolutionary biology
Background:
- Tomatoes exhibit diverse traits despite a limited genetic base.
- Transposable elements (TEs) are mobile genetic sequences with known roles in genome evolution.
Purpose of the Study:
- To investigate the contribution of transposable elements (TEs) to tomato diversity using whole-genome resequencing data.
- To identify TE insertions and their impact on gene expression and agronomic traits in tomatoes.
Main Methods:
- Whole-genome resequencing of 602 tomato accessions.
- Identification and characterization of transposable element insertion polymorphisms (TIPs).
- Genome-wide association studies (GWAS) to link TIPs with traits.
Main Results:
- Discovered 6,906 TE insertions polymorphisms (TIPs) from 337 TE families.
- TIPs are often found near genes related to environmental responses and influence transcript isoforms.
- Identified at least 40 TIPs associated with major agronomic traits and secondary metabolites.
Conclusions:
- Transposable element mobilization is a key driver of tomato diversification.
- TIPs play a significant role in shaping tomato phenotypes and offer valuable resources for crop improvement and breeding.
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