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De novo domestication of wild tomato using genome editing


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.

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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.

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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

Authors and Affiliations



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.

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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)

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Zsögön, A., Čermák, T., Naves, E. et al. De novo domestication of wild tomato using genome editing. Nat Biotechnol 36, 1211–1216 (2018).

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