Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Transient reprogramming of crop plants for agronomic performance

Nature Plants volume 7, pages 159–171 (2021)Cite this article

Subjects

Abstract

The development of a new crop variety is a time-consuming and costly process due to the reliance of plant breeding on gene shuffling to introduce desired genes into elite germplasm, followed by backcrossing. Here, we propose alternative technology that transiently targets various regulatory circuits within a plant, leading to operator-specified alterations of agronomic traits, such as time of flowering, vernalization requirement, plant height or drought tolerance. We redesigned techniques of gene delivery, amplification and expression around RNA viral transfection methods that can be implemented on an industrial scale and with many crop plants. The process does not involve genetic modification of the plant genome and is thus limited to a single plant generation, is broadly applicable, fast, tunable and versatile, and can be used throughout much of the crop cultivation cycle. The RNA-based reprogramming may be especially useful in plant pathogen pandemics but also for commercial seed production and for rapid adaptation of orphan crops.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Transfection of various crop plants with viral vectors delivered using Agrobacterium or as VPs.
Fig. 2: Induction and repression of flowering with viral vectors in several plant species.
Fig. 3: Modification of plant stature in several crop species via modulation of gibberellin metabolic pathway by viral vectors.
Fig. 4: Transient reprogramming of other agronomic traits in tomato with PVX vectors delivered by Agrobacterium using spraying.
Fig. 5: Enhanced virus spread, amplification and recombinant protein accumulation using modified PVX vectors.
Fig. 6: Fate of Agrobacterium and viral vectors in transfected plants and soil (greenhouse and open field).

Similar content being viewed by others

Data availability

All data generated or analysed during this study are included in this published article and its Supplementary Information. All materials are available for research purpose upon request from the corresponding author under a material transfer agreement with Nomad Bioscience. The following sequences of codon-optimized genes have been deposited in NCBI as GenBank accession numbers: MT877076 (SlTAGL1, codon optimized for rice), MT877077 (SlOVATE, codon optimized for rice), MT877078 (SlANT1, codon optimized for Bifidobacterium longum) and MT877079 (GFP, codon optimized for tobacco). Source data are provided with this paper.

References

  1. Marillonnet, S. et al. In planta engineering of viral RNA replicons: efficient assembly by recombination of DNA modules delivered by Agrobacterium. Proc. Natl Acad. Sci. USA 101, 6852–6857 (2004).

    Article  CAS  PubMed  Google Scholar 

  2. Marillonnet, S., Thoeringer, C., Kandzia, R., Klimyuk, V. & Gleba, Y. Systemic Agrobacterium tumefaciens‐mediated transfection of viral replicons for efficient transient expression in plants. Nat. Biotechnol. 23, 718–723 (2005).

    Article  CAS  PubMed  Google Scholar 

  3. Giritch, A. et al. Rapid high-yield expression of full-size IgG antibodies in plants coinfected with noncompeting viral vectors. Proc. Natl Acad. Sci. USA 103, 14701–14706 (2006).

    Article  CAS  PubMed  Google Scholar 

  4. Hahn, S., Giritch, A., Bartels, D., Bortesi, L. & Gleba, Y. A novel and fully scalable Agrobacterium spray-based process for manufacturing cellulases and other cost-sensitive proteins in plants. Plant Biotechnol. J. 13, 708–716 (2015).

    Article  CAS  PubMed  Google Scholar 

  5. Gleba, Y. Y., Tusé, D. & Giritch, A. Plant viral vectors for delivery by Agrobacterium. Curr. Top. Microbiol. Immunol. 375, 155–192 (2014).

    CAS  PubMed  Google Scholar 

  6. Lin, M. K. et al. Flowering locus T protein may act as the long-distance florigenic signal in the cucurbits. Plant Cell 19, 1488–1506 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. McGarry, R. C. & Ayre, B. G. Geminivirus-mediated delivery of florigen promotes determinate growth in aerial organs and uncouples flowering from photoperiod in cotton. PLoS ONE 7, e36746 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Yamagishi, N., Kishigami, R. & Yoshikawa, N. Reduced generation time of apple seedlings to within a year by means of a plant virus vector: a new plant-breeding technique with no transmission of genetic modification to the next generation. Plant Biotechnol. J. 12, 60–68 (2014).

    Article  CAS  PubMed  Google Scholar 

  9. Velázquez, K. et al. Precocious flowering of juvenile citrus induced by a viral vector based on citrus leaf blotch virus: a new tool for genetics and breeding. Plant Biotechnol. J. 14, 1976–1985 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Yuan, C. et al. Foxtail mosaic virus-induced flowering assays in monocot crops. J. Exp. Bot. 71, 3012–3023 (2020).

    Article  CAS  PubMed  Google Scholar 

  11. Pasin, F., Menzel, W. & Darós, J. A. Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses. Plant Biotechnol. J. 17, 1010–1026 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Turpen, T. H. et al. Malarial epitopes expressed on the surface of recombinant tobacco mosaic virus. Biotechnology 13, 53–57 (1995).

    CAS  PubMed  Google Scholar 

  13. Pogue, G. P., Lindbo, J. A., Garger, S. J. & Fitzmaurice, W. P. Making an ally from an enemy: plant virology and the new agriculture. Annu. Rev. Phytopathol. 40, 45–74 (2002).

    Article  CAS  PubMed  Google Scholar 

  14. Yamanaka, T. et al. Complete nucleotide sequence of the genomic RNA of tobacco mosaic virus strain Cg. Virus Genes 16, 173–176 (1998).

    Article  CAS  PubMed  Google Scholar 

  15. Liu, Y., Schiff, M., Marathe, R. & Dinesh-Kumar, S. P. Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus. Plant J. 30, 415–429 (2002).

    Article  CAS  PubMed  Google Scholar 

  16. Masuta, C. et al. Development of clover yellow vein virus as an efficient, stable gene-expression system for legume species. Plant J. 23, 539–546 (2000).

    Article  CAS  PubMed  Google Scholar 

  17. Wang, D. et al. Positional effect of gene insertion on genetic stability of a clover yellow vein virus-based expression vector. J. Gen. Plant Pathol. 69, 327–334 (2003).

    Article  CAS  Google Scholar 

  18. Chailakhyan, M. K. H. New facts in support of the hormonal theory of plant development. Compt. Rend. Acad. Sci. URSS 13, 79–83 (1936).

    Google Scholar 

  19. Andrés, F. & Coupland, G. The genetic basis of flowering responses to seasonal cues. Nat. Rev. Genet. 13, 627–639 (2012).

    Article  PubMed  Google Scholar 

  20. Corbesier, L. et al. FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316, 1030–1033 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Tamaki, S., Matsuo, S., Wong, H. L., Yokoi, S. & Shimamoto, K. Hd3a protein is a mobile flowering signal in rice. Science 316, 1033–1036 (2007).

    Article  CAS  PubMed  Google Scholar 

  22. Ream, T. S., Woods, D. P. & Amasino, R. M. The molecular basis of vernalization in different plant groups. Cold Spring Harb. Symp. Quant. Biol. 77, 105–115 (2012).

    Article  CAS  PubMed  Google Scholar 

  23. Luo, X. & He, Y. Experiencing winter for spring flowering: a molecular epigenetic perspective on vernalization. J. Integr. Plant Biol. 62, 104–117 (2020).

    Article  CAS  PubMed  Google Scholar 

  24. Peng, J. et al. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400, 256–261 (1999).

    Article  CAS  PubMed  Google Scholar 

  25. Sasaki, A. et al. Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416, 701–702 (2002).

    Article  CAS  PubMed  Google Scholar 

  26. Eshed, Y. & Lippman, Z. B. Revolutions in agriculture chart a course for targeted breeding of old and new crops. Science 366, eaax0025 (2019).

    Article  CAS  PubMed  Google Scholar 

  27. Sakamoto, T. et al. Genetic manipulation of gibberellin metabolism in transgenic rice. Nat. Biotechnol. 21, 909–913 (2003).

    Article  CAS  PubMed  Google Scholar 

  28. Suo, H. et al. Overexpression of AtDREB1A causes a severe dwarf phenotype by decreasing endogenous gibberellin levels in soybean [Glycine max (L.) Merr.]. PLoS ONE 7, e45568 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Achard, P. et al. The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism. Plant Cell 20, 2117–2129 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Hedden, P. & Sponsel, V. A century of gibberellin research. J. Plant Growth Regul. 34, 740–760 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Thomson, J. et al. Complementation of notabilis, an abscisic acid-deficient mutant of tomato: importance of sequence context and utility of partial complementation. Plant Cell Environ. 27, 459–471 (2004).

    Article  Google Scholar 

  32. Sah, S. K., Reddy, K. R. & Li, J. Abscisic acid and abiotic stress tolerance in crop plants. Front. Plant Sci. 7, 571 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Kasuga, M., Liu, Q., Miura, S., Yamaguchi-Shinozaki, K. & Shinozaki, K. Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat. Biotechnol. 17, 287–291 (1999).

    Article  CAS  PubMed  Google Scholar 

  34. Vaek, M. et al. Transgenic plants protected from insects. Nature 325, 33–37 (1987).

    Article  Google Scholar 

  35. Lifschitz, E. et al. The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. Proc. Natl Acad. Sci. USA 103, 6398–6403 (2006).

    Article  CAS  PubMed  Google Scholar 

  36. Liu, R. et al. DEMETER-like DNA demethylase governs tomato fruit ripening. Proc. Natl Acad. Sci. USA 112, 10804–10809 (2015).

    Article  CAS  PubMed  Google Scholar 

  37. Mathews, H. et al. Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport. Plant Cell 15, 1689–1703 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Butelli, E. et al. Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nat. Biotechnol. 26, 1301–1308 (2008).

    Article  CAS  PubMed  Google Scholar 

  39. Torti S., Schlesier R., Giritch A. & Gleba Y. Method of improving potexviral vector stability. European Patent EP3456829 A1 (2019).

  40. Marillonnet S., Engler C., Klimyuk V. & Gleba Y. Potexvirus-derived replicon. European Patent EP2061890 B1 (2012).

  41. Carvalho, S. L. et al. Construction of a full-length infectious cDNA clone of cowpea mild mottle virus. Virus Genes 53, 137–140 (2017).

    Article  CAS  PubMed  Google Scholar 

  42. Fujita, N. et al. N-terminal region of cysteine-rich protein (CRP) in carlaviruses is involved in the determination of symptom types. Mol. Plant Pathol. 19, 180–190 (2018).

    Article  CAS  PubMed  Google Scholar 

  43. Krimi, Z., Petit, A., Mougel, C., Dessaux, Y. & Nesme, X. Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils. Appl. Environ. Microbiol. 68, 3358–3365 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Cagliari, D. et al. Management of pest insects and plant diseases by non-transformative RNAi. Front. Plant Sci. 10, 1319 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  45. Mandell, D. J. et al. Biocontainment of genetically modified organisms by synthetic protein design. Nature 518, 55–60 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Bendandi, M. et al. Rapid, high-yield production in plants of individualized idiotype vaccines for non-Hodgkin’s lymphoma. Ann. Oncol. 21, 2420–2427 (2010).

    Article  CAS  PubMed  Google Scholar 

  47. Roemer P., Bortesi L., Tiede D., Giritch A. & Gleba Y. Agrobacterium for transient transfection of whole plants. European Patent EP2834362 B1 (2018).

  48. Yambao, M. L. et al. Point mutations in helper component protease of clover yellow vein virus are associated with the attenuation of RNA-silencing suppression activity and symptom expression in broad bean. Arch. Virol. 153, 105–115 (2008).

    Article  CAS  PubMed  Google Scholar 

  49. Seo, J., Lee, H. & Kim, K. Systemic gene delivery into soybean by simple rub-inoculation with plasmid DNA of a soybean mosaic virus-based vector. Arch. Virol. 154, 1575 (2009).

    Article  CAS  Google Scholar 

  50. Bouton, C. et al. Foxtail mosaic virus: a viral vector for protein expression in cereals. Plant Physiol. 177, 1352–1367 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Bergau, N., Bennewitz, S., Syrowatka, F., House, G. & Tissier, A. The development of type VI glandular trichomes in the cultivated tomato S. lycopersicum and a related wild species S. habrochaites. BMC Plant Biol. 15, 289 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Eggert, K. & von Wirén, N. Response of the plant hormone network to boron deficiency. New Phytol. 216, 868–881 (2017).

    Article  CAS  PubMed  Google Scholar 

  53. Lee, J., Durst, R. W. & Wrolstad, R. E. Determination of total monomeric anthocyanin pigment content of fruit juices, beverages, natural colorants, and wines by the pH differential method: collaborative study. J. AOAC Int. 88, 1269–1278 (2005).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank E.-M. Franken (Bayer CropScience) for encouragement and valuable advice on experiments and H. Haydon (Kentucky BioProcessing) for support in conducting field trials. We also thank our colleagues at Nomad Bioscience and Icon Genetics, C. Engler, K. Havranek, T.-M. Ehnert, V. Klimyuk, F. Thieme, R. Kandzia, A. Nickstadt, Y. Symonenko and E. Stegemann-Oelerich for their valuable help. We are grateful to E. Hiatt, J. Poole, J. W. Shepherd and E. Blandford (Kentucky BioProcessing) for their help in conducting field trials. We thank T. Matsumura and I. Uyeda (Hokkaido University) for the plasmid pClYVV-GFP received as a gift, M. Quint (Martin Luther University Halle-Wittenberg) for providing several Arabidopsis ecotypes and M. Köck (Martin Luther University Halle-Wittenberg) for providing climatic cabinets for plant growth. We thank K. Eggert and B. Kettig (IPK-Gatersleben) for phytohormone analysis and A. Steppuhn (Free University Berlin) for providing hornworm eggs. We thank D. Tusé (DT/Consulting Group) and N. Amrhein (ETH Zürich) for critical reading of manuscript. Part of this work has been financially supported by Bayer CropScience. K.K. and V.P. acknowledge financial support by the Institute Strategic Programmme grant ‘Designing Future Wheat’ (BB/P016855/1) from the Biotechnology and Biological Sciences Research Council of the United Kingdom.

Author information

Author notes

  1. Stefan Werner

    Present address: Icon Genetics GmbH, Halle, Germany

  2. These authors contributed equally: S. Torti, R. Schlesier.

Authors and Affiliations

  1. Nomad Bioscience GmbH, Halle, Germany

    Stefano Torti, René Schlesier, Anka Thümmler, Doreen Bartels, Patrick Römer, Birgit Koch, Stefan Werner, Anatoli Giritch & Yuri Gleba

  2. Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK

    Vinay Panwar & Kostya Kanyuka

  3. Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Germany

    Nicolaus von Wirén

  4. The Sainsbury Laboratory, University of East Anglia, Norwich, UK

    Jonathan D. G. Jones

  5. Biocenter, Electron Microscopy, Martin Luther University of Halle-Wittenberg, Halle, Germany

    Gerd Hause

Authors
  1. Stefano Torti
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. René Schlesier
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anka Thümmler
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Doreen Bartels
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Patrick Römer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Birgit Koch
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Stefan Werner
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Vinay Panwar
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Kostya Kanyuka
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Nicolaus von Wirén
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Jonathan D. G. Jones
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Gerd Hause
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Anatoli Giritch
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Yuri Gleba
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.G. conceptualized and supervised the research. Y.G. and A.G. directed the research. Y.G., A.G., S.T., R.S., A.T., P.R., S.W. and K.K. designed the research. S.T., R.S., A.T., D.B., P.R., B.K., S.W., V.P. and G.H. performed the research. Y.G., A.G., S.T., R.S., A.T., P.R., B.K., S.W., V.P., K.K., J.D.G.J., N.v.W. and G.H. analysed the data. Y.G., A.G., S.T. and R.S. wrote the paper. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Anatoli Giritch.

Ethics declarations

Competing interests

Y.G. has shares in Nomad Bioscience. S.T., R.S., A.T., D.B., P.R., B.K., A.G. and Y.G. are employed by Nomad Bioscience. S.W. has been employed by Nomad Bioscience. A.G., D.B., P.R. and Y.G. are inventors on the patent application entitled ‘Process of transfecting plants’ (European patent no. EP2601295 B1); P.R., D.B., A.G. and Y.G. are inventors on the patent application ‘Agrobacterium for transient transfection of whole plant’ (European patent no. EP2834362 B1); Y.G. is an inventor on the patent application ‘Potexvirus-derived replicon’ (European patent no. EP2061890 B1); A.T., D.B., A.G. and Y.G. are inventors on the patent application ‘Process of providing plants with abiotic stress resistance’ (European patent no. EP2999790 B1); and S.T, R.S., A.G. and Y.G. are inventors on the patent application ‘Method of improving potexviral vector stability’ (European patent no. EP3456829 A1). The ownership of the patents resides with Nomad Bioscience. The authors have no other competing interests.

Additional information

Peer review information Nature Plants thanks Stanton Gelvin, Lee Hickey and Peter Langridge for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–8, Tables 1–5, unprocessed SDS gels, western blots and agarose gels for Supplementary Figs. 4, 7 and 8, and statistical source data for Supplementary Figs. 3–7.

Reporting Summary

Supplementary Table

Statistical source data of all the graphs of Supplementary Figs. 3–7.

Source data

Source Data Fig. 2

Unprocessed SDS gel and western blot for Fig. 2c.

Source Data Fig. 2

Statistical source data.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Unprocessed agarose gels for Fig. 5a; SDS gel for Fig. 5g,d.

Source Data Fig. 5

Statistical source data.

Source Data Fig. 6

Unprocessed agarose gels for Fig. 6a,c,d.

Source Data Fig. 6

Statistical source data.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Torti, S., Schlesier, R., Thümmler, A. et al. Transient reprogramming of crop plants for agronomic performance. Nat. Plants 7, 159–171 (2021). https://doi.org/10.1038/s41477-021-00851-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-021-00851-y

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing