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A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening

Nature Genetics volume 38, pages 948952 (2006) | Download Citation



A major component in the regulatory network controlling fruit ripening is likely to be the gene at the tomato Colorless non-ripening (Cnr) locus1,2. The Cnr mutation results in colorless fruits with a substantial loss of cell-to-cell adhesion. The nature of the mutation and the identity of the Cnr gene were previously unknown. Using positional cloning and virus-induced gene silencing, here we demonstrate that an SBP-box (SQUAMOSA promoter binding protein–like) gene resides at the Cnr locus. Furthermore, the Cnr phenotype results from a spontaneous epigenetic change in the SBP-box promoter. The discovery that Cnr is an epimutation was unexpected, as very few spontaneous epimutations have been described in plants3,4. This study demonstrates that an SBP-box gene is critical for normal ripening and highlights the likely importance of epialleles in plant development and the generation of natural variation.

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We would like to thank P. Meyer and P. Walley for useful discussions, S. Butcher and J. Abbott for assistance with annotation of the tomato genomic sequences, D. Baulcombe for providing the original PVX vector, and the Biotechnology and Biological Sciences Research Council (UK) for financial support.

Author information


  1. Warwick Horticulture Research International (HRI), University of Warwick, Wellesbourne, Warwick CV35 9EF, UK.

    • Kenneth Manning
    • , Mahmut Tör
    • , Yiguo Hong
    •  & Andrew J Thompson
  2. Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.

    • Mervin Poole
    •  & Graham B Seymour
  3. Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.

    • Graham J King
  4. US Department of Agriculture–Agricultural Research Service and Boyce Thompson Institute for Plant Science Research, Cornell University, Tower Road, Ithaca, New York 14853-2901, USA.

    • James J Giovannoni


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K.M. performed research, designed experiments and wrote the paper; M.T. performed research and designed experiments; M.P. performed research; Y.H. designed and performed VIGS experiments and wrote the paper; A.J.T. performed research and designed experiments; G.K. designed experiments; J.J.G. designed experiments and wrote the paper; and G.B.S. initiated the project, designed experiments and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Graham B Seymour.

Supplementary information

PDF files

  1. 1.

    Supplementary Figure 1

    Phylogenetic relationship between the tomato LeSPL-CNR protein and SBP-box proteins from Arabidopsis (AtSPL1, AtSPL3, AtSPL4,AtSPL5, AtSPL12), Antirrhinum (AmSBP1, AmSBP2), Betula (BpSPL1)and cotton (GhSBP).

  2. 2.

    Supplementary Table 1

    Primer sequences for genetic mapping experiments, quantitative real-time RT-PCR and construction of VIGS vector.

  3. 3.

    Supplementary Table 2

    Primer sequences for bisulfite sequencing.

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