Abstract

Genome editing technologies are being widely adopted in plant breeding1. However, a looming challenge of engineering desirable genetic variation in diverse genotypes is poor predictability of phenotypic outcomes due to unforeseen interactions with pre-existing cryptic mutations2,3,4. In tomato, breeding with a classical MADS-box gene mutation that improves harvesting by eliminating fruit stem abscission frequently results in excessive inflorescence branching, flowering and reduced fertility due to interaction with a cryptic variant that causes partial mis-splicing in a homologous gene5,6,7,8. Here, we show that a recently evolved tandem duplication carrying the second-site variant achieves a threshold of functional transcripts to suppress branching, enabling breeders to neutralize negative epistasis on yield. By dissecting the dosage mechanisms by which this structural variant restored normal flowering and fertility, we devised strategies that use CRISPR–Cas9 genome editing to predictably improve harvesting. Our findings highlight the under-appreciated impact of epistasis in targeted trait breeding and underscore the need for a deeper characterization of cryptic variation to enable the full potential of genome editing in agriculture.

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Data availability

The DNA sequencing data used to map branching QTLs in the S. lycopersicum j2 ej2W × S. lycopersicum Fla.8924 F2 population and the RNA sequencing data of transition and floral meristem stages for S. lycopersicum M82, S. lycopersicum j2 ej2W and S. lycopersicum Fla.8924 has been deposited in SRA (http://ncbi.nlm.nih.gov/sra) under the accession code PRJNA509653.

Source Data files for all main and supplementary figures are available in the online version of the paper. All additional data sets are available from the corresponding author on request.

Additional information

Journal peer review information: Nature Plants thanks Allen Van Deynze, Jianbing Yan and the other anonymous reviewer(s) 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.

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Acknowledgements

We thank all members of the Lippman laboratory for valuable discussions. We thank A. Krainer, J. Dalrymple, G. Robitaille and J. Kim for technical support. We thank K. Swartwood for assistance with tomato transformation. We thank T. Mulligan, S. Vermylen, A. Krainer, S. Qiao and K. Schlecht, from CSHL, and staff from Cornell University’s Long Island Horticultural Research and Extension Center, for assistance with plant care. We thank S. Goodwin, S. Muller, R. Wappel and E. Ghiban from the CSHL Genome Center for sequencing support. We thank D. Zamir (Hebrew University, Israel) and E. van der Knaap (University of Georgia) for providing seed. This research was supported by an EMBO Long-Term Fellowship (no. ALTF 1589-2014) to S.S., a National Science Foundation Postdoctoral Research Fellowship in Biology Grant (no. IOS-1523423) to Z.H.L., a National Institute of Health Research Project with Complex Structure Cooperative Agreement (3UM1HG008898-01S2) to F.J.S., the ANR grant tomaTE (no. ANR-17-CE20-0024-02) to J.M.J.-G., a Research Grant from BARD (no. IS-4818-15), the United States–Israel Binational Agricultural Research and Development Fund, to Z.B.L., an Agriculture and Food Research Initiative competitive grant no. 2016-67013-24452 of the USDA National Institute of Food and Agriculture to S.H and Z.B.L. and the National Science Foundation Plant Genome Research Program (no. IOS-1732253) to J.V.E., M.C.S. and Z.B.L.

Author information

Affiliations

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

    • Sebastian Soyk
    • , Zachary H. Lemmon
    •  & Zachary B. Lippman
  2. Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA

    • Fritz J. Sedlazeck
  3. Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France

    • José M. Jiménez-Gómez
  4. Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA

    • Michael Alonge
    •  & Michael C. Schatz
  5. Horticultural Sciences Department, University of Florida, Wimauma, FL, USA

    • Samuel F. Hutton
  6. The Boyce Thompson Institute, Ithaca, NY, USA

    • Joyce Van Eck
  7. Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA

    • Joyce Van Eck
  8. Department of Oncologye, Johns Hopkins Medicine, Baltimore, MD, USA

    • Michael C. Schatz
  9. Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    • Zachary B. Lippman

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Contributions

S.S., Z.H.L, F.J.S., J.M.J.-G., S.H., J.V.E., M.C.S. and Z.B.L. designed and planned experiments. S.S., Z.H.L, F.J.S., J.M.J.-G., S.H. and Z.B.L. performed experiments and collected the data. S.S., Z.H.L, F.J.S., J.M.J.-G., M.A., M.C.S. and Z.B.L. analysed the data. S.S., Z.H.L. and Z.B.L. designed the research. S.S. and Z.B.L. wrote the paper with the input from all authors.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Sebastian Soyk or Zachary B. Lippman.

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https://doi.org/10.1038/s41477-019-0422-z