Ensuring effective removal of transgenes before release of genome-edited crops

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Ensuring effective removal of transgenes before release of genome-edited crops

Genome editing technology is evolving fast, and many labs worldwide are generating crop plants with improved traits. If transgenes were used to generate the edits, foreign DNA must be effectively removed by outcrossing. After an evaluation of various technologies, we show that long-read whole-genome sequencing (WGS) is at present the only reliable approach to confirm the absence of foreign DNA. We suggest using long-read WGS before requesting exemption from classification as genetically modified organisms and provide a guide for interpreting WGS data.

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Acknowledgements

This work was supported in parts by the Gates Foundation to H.H.U. (Investment ID INV-008733 and Investment ID INV-063189), Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy – EXC-2048/1 – project ID 390686111 (CEPLAS), and an Alexander von Humboldt Professorship (W.F.).

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Author notes

  1. These authors contributed equally: Jose C. Huguet-Tapia, Eliza P. I. Loo.

Authors and Affiliations

  1. Department of Plant Pathology, University of Florida Gainesville, Gainesville, FL, USA

    Jose C. Huguet-Tapia & Frank F. White

  2. Institute for Molecular Physiology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Eliza P. I. Loo, Marcel Buchholzer, Thomas Hartwig & Wolf B. Frommer

  3. Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany

    Eliza P. I. Loo & Wolf B. Frommer

  4. Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA

    Bing Yang

  5. Donald Danforth Plant Science Center, St. Louis, MO, USA

    Bing Yang

  6. Institute for Transformative Biomolecules (ITbM), Nagoya, Japan

    Wolf B. Frommer

Authors

  1. Jose C. Huguet-Tapia
  2. Eliza P. I. Loo
  3. Marcel Buchholzer
  4. Thomas Hartwig
  5. Bing Yang
  6. Frank F. White
  7. Wolf B. Frommer

Contributions

W.F., F.F.W. and B.Y. conceived of the study, J.H.T., E.L., T.H., B.Y. and F.F.W. were instrumental for the WGS analyses and evaluation of different technologies, E.P. & W.F. were responsible for all aspects of standard technologies (such as PCR and DNA gel blotting), and M.B., B.Y. and W.F. were responsible for compliance with country-specific regulations. J.H.T., E.L. and W.F. wrote the manuscript, and all authors were involved in revisions.

Corresponding author

Correspondence to Wolf B. Frommer.

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Competing interests

The authors declare no competing interests.

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Huguet-Tapia, J.C., Loo, E.P.I., Buchholzer, M. et al. Ensuring effective removal of transgenes before release of genome-edited crops. Nat Biotechnol 43, 1603–1605 (2025). https://doi.org/10.1038/s41587-025-02805-7

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  • DOI: https://doi.org/10.1038/s41587-025-02805-7