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

Abstract

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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Figure 1: High-resolution mapping of the Cnr locus.
Figure 2: Expression of ORF 7 in wild-type and mutant fruits.
Figure 3: An epigenetic change at the Cnr locus.
Figure 4: Percentage cytosine methylation at CpG, CpNpG and asymmetric cytosines upstream of the first ATG of ORF 7 determined by bisulfite sequencing of fruit and leaf tissues.
Figure 5: PVX-mediated VIGS of LeSPL-CNR in fruit attached to tomato plant.

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Acknowledgements

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.

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Authors and Affiliations

Authors

Contributions

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.

Corresponding author

Correspondence to Graham B Seymour.

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The authors declare no competing financial interests.

Supplementary information

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). (PDF 12 kb)

Supplementary Table 1

Primer sequences for genetic mapping experiments, quantitative real-time RT-PCR and construction of VIGS vector. (PDF 52 kb)

Supplementary Table 2

Primer sequences for bisulfite sequencing. (PDF 57 kb)

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Manning, K., Tör, M., Poole, M. et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38, 948–952 (2006). https://doi.org/10.1038/ng1841

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