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:

De novo domestication of wild tomato using genome editing

Nature Biotechnology volume 36, pages 1211–1216 (2018)Cite this article

Subjects

Abstract

Breeding of crops over millennia for yield and productivity1 has led to reduced genetic diversity. As a result, beneficial traits of wild species, such as disease resistance and stress tolerance, have been lost2. We devised a CRISPR–Cas9 genome engineering strategy to combine agronomically desirable traits with useful traits present in wild lines. We report that editing of six loci that are important for yield and productivity in present-day tomato crop lines enabled de novo domestication of wild Solanum pimpinellifolium. Engineered S. pimpinellifolium morphology was altered, together with the size, number and nutritional value of the fruits. Compared with the wild parent, our engineered lines have a threefold increase in fruit size and a tenfold increase in fruit number. Notably, fruit lycopene accumulation is improved by 500% compared with the widely cultivated S. lycopersicum. Our results pave the way for molecular breeding programs to exploit the genetic diversity present in wild plants.

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

Figure 1: Plant morphology and fruit shape in de novo domesticated S. pimpinellifolium plants.
Figure 2: Flower number and fruit size in de novo domesticated S. pimpinellifolium plants.
Figure 3: Nutritional content of fruits from engineered S. pimpinellifolium plants.

Similar content being viewed by others

References

  1. Evans, L.T. Crop Evolution, Adaptation and Yield (Cambridge Univ. Press, 1996).

  2. van de Wouw, M., Kik, C., van Hintum, T., van Treuren, R. & Visser, B. Genetic erosion in crops: concept, research results and challenges. Plant Genet. Resour. 8, 1–15 (2010).

    Article  Google Scholar 

  3. Food and Agriculture Organization of the United Nations. FAO Statistical Yearbook 2015: World Food and Agriculture (United Nations, 2015).

  4. Lippman, Z. & Tanksley, S.D. Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics 158, 413–422 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Gruber, K. Agrobiodiversity: the living library. Nature 544, S8–S10 (2017).

    Article  CAS  PubMed  Google Scholar 

  6. Meyer, R.S. & Purugganan, M.D. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840–852 (2013).

    Article  CAS  PubMed  Google Scholar 

  7. Cˇermák, T. et al. A multipurpose toolkit to enable advanced genome engineering in plants. Plant Cell 29, 1196–1217 (2017).

    Article  CAS  Google Scholar 

  8. Falke, K.C. et al. The spectrum of mutations controlling complex traits and the genetics of fitness in plants. Curr. Opin. Genet. Dev. 23, 665–671 (2013).

    Article  CAS  PubMed  Google Scholar 

  9. Zsögön, A., Cermak, T., Voytas, D. & Peres, L.E.P. Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: case study in tomato. Plant Sci. 256, 120–130 (2017).

    Article  CAS  PubMed  Google Scholar 

  10. Pnueli, L. et al. The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125, 1979–1989 (1998).

    CAS  PubMed  Google Scholar 

  11. Liu, J., Van Eck, J., Cong, B. & Tanksley, S.D. A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc. Natl. Acad. Sci. USA 99, 13302–13306 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Xu, C. et al. A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat. Genet. 47, 784–792 (2015).

    Article  CAS  PubMed  Google Scholar 

  13. Frary, A. et al. Fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289, 85–88 (2000).

    Article  CAS  PubMed  Google Scholar 

  14. Lippman, Z.B. et al. The making of a compound inflorescence in tomato and related nightshades. PLoS Biol. 6, e288 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Ronen, G., Carmel-Goren, L., Zamir, D. & Hirschberg, J. An alternative pathway to β-carotene formation in plant chromoplasts discovered by map-based cloning of beta and old-gold color mutations in tomato. Proc. Natl. Acad. Sci. USA 97, 11102–11107 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Rick, C.M. The tomato. Sci. Am. 239, 76–87 (1978).

    Article  Google Scholar 

  17. Peet, M.M. Fruit cracking in tomato. Horttechnology 2, 216–223 (1991).

    Article  Google Scholar 

  18. Cong, B., Barrero, L.S. & Tanksley, S.D. Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat. Genet. 40, 800–804 (2008).

    Article  CAS  PubMed  Google Scholar 

  19. Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017).

    Article  CAS  PubMed  Google Scholar 

  20. Römer, S. et al. Elevation of the provitamin A content of transgenic tomato plants. Nat. Biotechnol. 18, 666–669 (2000).

    Article  PubMed  Google Scholar 

  21. Clinton, S.K. Lycopene: chemistry, biology, and implications for human health and disease. Nutr. Rev. 56, 35–51 (2009).

    Article  Google Scholar 

  22. Bramley, P.M. Is lycopene beneficial to human health? Phytochemistry 54, 233–236 (2000).

    Article  CAS  PubMed  Google Scholar 

  23. Lenucci, M.S., Cadinu, D., Taurino, M., Piro, G. & Dalessandro, G. Antioxidant composition in cherry and high-pigment tomato cultivars. J. Agric. Food Chem. 54, 2606–2613 (2006).

    Article  CAS  PubMed  Google Scholar 

  24. Kuti, J.O. & Konuru, H.B. Effects of genotype and cultivation environment on lycopene content in red-ripe tomatoes. J. Sci. Food Agric. 85, 2021–2026 (2005).

    Article  CAS  Google Scholar 

  25. Adalid, A.M., Roselló, S. & Nuez, F. Evaluation and selection of tomato accessions (Solanum section Lycopersicon) for content of lycopene, β-carotene and ascorbic acid. J. Food Compos. Anal. 23, 613–618 (2010).

    Article  CAS  Google Scholar 

  26. Ashrafi, H., Kinkade, M.P., Merk, H.L. & Foolad, M.R. Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population. Mol. Breed. 30, 549–567 (2012).

    Article  CAS  Google Scholar 

  27. Liu, Y.-S. There is more to tomato fruit colour than candidate carotenoid genes. Plant Biotechnol. J. 1, 195–207 (2003).

    Article  CAS  PubMed  Google Scholar 

  28. Li, C. et al. RNA-guided Cas9 as an in vivo desired-target mutator in maize. Plant Biotechnol. J. 15, 1566–1576 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Soyk, S. et al. Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169, 1142–1155.e12 (2017).

    Article  CAS  PubMed  Google Scholar 

  30. Doebley, J.F., Gaut, B.S. & Smith, B.D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006).

    Article  CAS  PubMed  Google Scholar 

  31. Doebley, J., Stec, A. & Hubbard, L. The evolution of apical dominance in maize. Nature 386, 485–488 (1997).

    Article  CAS  PubMed  Google Scholar 

  32. Studer, A., Zhao, Q., Ross-Ibarra, J. & Doebley, J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43, 1160–1163 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Moreno, M.A., Harper, L.C., Krueger, R.W., Dellaporta, S.L. & Freeling, M. liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis. Genes Dev. 11, 616–628 (1997).

    Article  CAS  PubMed  Google Scholar 

  34. Wang, H., Studer, A.J., Zhao, Q., Meeley, R. & Doebley, J.F. Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in tga1. Genetics 200, 965–974 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Yang, Q. et al. CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. Proc. Natl. Acad. Sci. USA 110, 16969–16974 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Huang, C. et al. ZmCCT9 enhances maize adaptation to higher latitudes. Proc. Natl. Acad. Sci. USA 115, E334–E341 (2018).

    Article  CAS  PubMed  Google Scholar 

  37. Tian, Z. et al. Artificial selection for determinate growth habit in soybean. Proc. Natl. Acad. Sci. USA 107, 8563–8568 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Cai, Y. et al. CRISPR/Cas9-mediated targeted mutagenesis of GmFT2a delays flowering time in soya bean. Plant Biotechnol. J. 16, 176–185 (2018).

    Article  CAS  PubMed  Google Scholar 

  39. Lu, X. et al. The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication. Plant J. 86, 530–544 (2016).

    Article  CAS  PubMed  Google Scholar 

  40. Dong, Y. et al. Pod shattering resistance associated with domestication is mediated by a NAC gene in soybean. Nature Commun. 5, 3352 (2014).

    Article  CAS  Google Scholar 

  41. Pino, L.E. et al. The Rg1 allele as a valuable tool for genetic transformation of the tomato 'Micro-Tom' model system. Plant Methods 6, 23 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Murashige, T. & Skoog, F. A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol. Plant. 15, 473–497 (1962).

    Article  CAS  Google Scholar 

  43. Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641 (2012).

  44. Sérino, S., Gomez, L., Costagliola, G. & Gautier, H. HPLC assay of tomato carotenoids: validation of a rapid microextraction technique. J. Agric. Food Chem. 57, 8753–8760 (2009).

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to S. Schültke for technical assistance. This work was supported by funding from the Agency for the Support and Evaluation of Graduate Education (CAPES, Brazil), the National Council for Scientific and Technological Development (CNPq, Brazil) and Foundation for Research Assistance of the São Paulo State (FAPESP, Brazil), and the German Federal Ministry of Education and Research (BMBF, Germany). We thank CAPES for studentships granted to E.R.N. and FAPESP for the studentship granted to M.M.N. (2013/12209-1). L.F. was supported by FAPESP grant 2013/18056-2. FAPESP and BMBF provided a grant for L.E.P.P. (2015/50220-2) and J.K. (031B0334). L.E.P.P. acknowledges a grant from CNPq (grant 307040/2014-3).

Author information

Author notes

  1. Tomáš Čermák

    Present address: Present address: Inari Agriculture, Cambridge, Massachusetts, USA.,

  2. Agustin Zsögön and Tomáš Čermák: These authors contributed equally to this work.

Authors and Affiliations

  1. Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil

    Agustin Zsögön & Emmanuel Rezende Naves

  2. Department of Genetics, Cell Biology and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA

    Tomáš Čermák & Daniel F Voytas

  3. Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz,” Universidade de São Paulo, Piracicaba, Brazil

    Marcela Morato Notini & Lázaro Eustáquio Pereira Peres

  4. Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Münster, Germany

    Kai H Edel, Stefan Weinl & Jörg Kudla

  5. Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil

    Luciano Freschi

Authors
  1. Agustin Zsögön
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tomáš Čermák
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Emmanuel Rezende Naves
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marcela Morato Notini
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kai H Edel
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Stefan Weinl
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Luciano Freschi
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Daniel F Voytas
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jörg Kudla
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Lázaro Eustáquio Pereira Peres
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.Z., T.C., D.F.V., J.K. and L.E.P.P. designed the study. A.Z., T.C., M.M.N., E.R.N., K.H.E., S.W. and L.F. performed experiments. A.Z., T.C. and K.H.E. analyzed data. A.Z., K.H.E., J.K. and L.E.P.P. prepared the manuscript. All authors have revised and approved the final version of the manuscript.

Corresponding authors

Correspondence to Jörg Kudla or Lázaro Eustáquio Pereira Peres.

Ethics declarations

Competing interests

After completion of this work in the laboratory of D.F.V., T.C. became an employee of Inari Agriculture, a company that uses novel technologies for crop breeding. D.F.V. is a founder and Chief Science Officer of Calyxt, a company applying genome editing to plants.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 (PDF 16905 kb)

Life Sciences Reporting Summary (PDF 130 kb)

Supplementary Tables

Supplementary Tables 1–12 (PDF 1582 kb)

Supplementary Note 1

Annotated sequence for pTC321 (TXT 57 kb)

Supplementary Note 2

Annotated sequence for pTC603 (TXT 41 kb)

Supplementary Dataset 1

Raw sequence files and alignments corresponding to Supplementary Figure 2 and Supplementary Tables 3 and 5 (ZIP 53625 kb)

Supplementary Dataset 2

Raw sequence files and alignments corresponding to Figures 1–3, Supplementary Figures 3, 4, 5 and 7, and Supplementary Table 2 (ZIP 37477 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zsögön, A., Čermák, T., Naves, E. et al. De novo domestication of wild tomato using genome editing. Nat Biotechnol 36, 1211–1216 (2018). https://doi.org/10.1038/nbt.4272

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.4272

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