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.

Rapid improvement of domestication traits in an orphan crop by genome editing

Abstract

Genome editing holds great promise for increasing crop productivity, and there is particular interest in advancing breeding in orphan crops, which are often burdened by undesirable characteristics resembling wild relatives. We developed genomic resources and efficient transformation in the orphan Solanaceae crop ‘groundcherry’ (Physalis pruinosa) and used clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein-9 nuclease (Cas9) (CRISPR–Cas9) to mutate orthologues of tomato domestication and improvement genes that control plant architecture, flower production and fruit size, thereby improving these major productivity traits. Thus, translating knowledge from model crops enables rapid creation of targeted allelic diversity and novel breeding germplasm in distantly related orphan crops.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Fig. 1: The orphan Solanaceae crop P. pruinosa (groundcherry) exhibits similar traits to the wild tomato species S. pimpinellifolium.
Fig. 2: CRISPR–Cas9 targeting of domestication and improvement-related genes in P. pruinosa.
Fig. 3: CRISPR–Cas9 targeting of domestication and improvement-related gene CLV1 in P. pruinosa.

Similar content being viewed by others

Data availability

Raw data from this study have been submitted to the National Center for Biotechnology Information Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP142654. Transcriptome and genome assemblies have been deposited at the Sol Genomics Network (ftp://ftp.solgenomics.net).

References

  1. Scheben, A., Wolter, F., Batley, J., Puchta, H. & Edwards, D. New Phytol. 216, 682–698 (2017).

    Article  CAS  Google Scholar 

  2. Bohra, A., Jha, U. C., Kishor, P. B. K., Pandey, S. & Singh, N. P. Biotechnol. Adv. 32, 1410–1428 (2014).

    Article  CAS  Google Scholar 

  3. Wolff, X. Y. HortScience 26, 1558–1559 (1991).

    Google Scholar 

  4. Särkinen, T., Bohs, L., Olmstead, R. G. & Knapp, S. BMC Evol. Biol. 13, 214 (2013).

    Article  Google Scholar 

  5. Van der Knaap, E. et al. Front. Plant Sci. 5, 227 (2014).

    Article  Google Scholar 

  6. Soyk, S. et al. Nat. Genet. 49, 162–168 (2017).

    Article  CAS  Google Scholar 

  7. Menzel, M. Y. Proc. Am. Phil. Soc. 95, 132–183 (1951).

    Google Scholar 

  8. Paran, I. & van der Knaap, E. J. Exp. Bot. 58, 3841–3852 (2007).

    Article  CAS  Google Scholar 

  9. Van Eck, J. Curr. Opin. Biotechnol. 49, 35–41 (2018).

    Article  CAS  Google Scholar 

  10. Brooks, C., Nekrasov, V., Lippman, Z. B. & Van Eck, J. Plant Physiol. 166, 1292–1297 (2014).

    Article  Google Scholar 

  11. Garzón-Martínez, Ga, Zhu, Z. I., Landsman, D., Barrero, L. S. & Mariño-Ramírez, L. BMC Genomics 13, 151 (2012).

    Article  Google Scholar 

  12. Xu, C. et al. Nat. Genet. 47, 784–792 (2015).

    Article  CAS  Google Scholar 

  13. Soyk, S. et al. Cell 169, 1142–1155 (2017).

    Article  CAS  Google Scholar 

  14. Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. Bioinformatics 31, 3210–3212 (2015).

    Article  Google Scholar 

  15. Park, S. J., Eshed, Y. & Lippman, Z. B. Curr. Opin. Plant Biol. 17, 70–77 (2014).

    Article  Google Scholar 

  16. Pnueli, L. et al. Development 125, 1979–1989 (1998).

    CAS  PubMed  Google Scholar 

  17. Rodríguez-Leal, D., Lemmon, Z. H., Man, J., Bartlett, M. E. & Lippman, Z. B. Cell 171, 470–480 (2017).

    Article  Google Scholar 

  18. Cermak, T. et al. Plant Cell 29, 1196–1217 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Altpeter, F. et al. Plant Cell 28, 1510–1520 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Lowe, K. et al. Plant Cell 28, 1998–2015 (2016).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank members of the Lippman and Van Eck laboratories for valuable discussions. We thank T. Mulligan, S. Vermylen, A. Krainer and S. Qiao for assistance with plant care. We thank C. Pei for assistance with CRISPR analysis. This research was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology grant (IOS-1523423) to Z.H.L., and the National Science Foundation Plant Genome Research Program (IOS-1732253) to J.V.E. and Z.B.L.

Author information

Authors and Affiliations

Authors

Contributions

Z.H.L., N.T.R., J.D., J.V.E. and Z.B.L. designed and planned the experiments. All authors performed the experiments and collected the data. Z.H.L performed all bioinformatics analyses. All authors analysed the data. Z.H.L., J.V.E. and Z.B.L. designed the research. Z.H.L., S.S., J.V.E. and Z.B.L. wrote the paper with input from all authors.

Corresponding authors

Correspondence to Joyce Van Eck or Zachary B. Lippman.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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

Supplementary information

Supplementary Information

Methods, Supplementary Figure 1 and Supplementary Table 1

Reporting Summary

Supplementary Data

Raw quantification data for Figure 2 and Supplementary Figure 1

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lemmon, Z.H., Reem, N.T., Dalrymple, J. et al. Rapid improvement of domestication traits in an orphan crop by genome editing. Nature Plants 4, 766–770 (2018). https://doi.org/10.1038/s41477-018-0259-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-018-0259-x

This article is cited by

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