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

Nature Plants volume 4, pages766–770(2018)Cite this article

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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.

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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.

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).

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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.

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Author notes

  1. These authors contributed equally: Nathan T. Reem, Justin Dalrymple, Sebastian Soyk.

Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Zachary H. Lemmon, Justin Dalrymple, Sebastian Soyk, Daniel Rodriguez-Leal & Zachary B. Lippman

  2. The Boyce Thompson Institute, Ithaca, NY, USA

    Nathan T. Reem, Kerry E. Swartwood & Joyce Van Eck

  3. Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA

    Joyce Van Eck

  4. Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Zachary B. Lippman

Authors
  1. Zachary H. Lemmon
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  2. Nathan T. Reem
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  3. Justin Dalrymple
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  4. Sebastian Soyk
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  5. Kerry E. Swartwood
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  6. Daniel Rodriguez-Leal
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  7. Joyce Van Eck
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  8. Zachary B. Lippman
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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.

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The authors declare no competing interests.

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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

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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

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