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Comparative WGBS identifies genes that influence non-ripe phenotype in tomato epimutant Colourless non-ripening

Abstract

Whole-genome bisulfite sequencing (WGBS) allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals. This technology provides a powerful tool to identify genes that are potentially controlled by dynamic changes of DNA methylation and demethylation. However, naturally occurring epimutants are rare and genes under epigenetic regulation as well as their biological relevances are often difficult to define. In tomato, fruit development and ripening are a complex process that involves epigenetic control. We have taken the advantage of the tomato epimutant Colourless non-ripening (Cnr) and performed comparative mining of the WGBS datasets for the Cnr and SlCMT3-silenced Cnr fruits. We compared DNA methylation profiles for the promoter sequences of approximately 5,000 bp immediately upstream of the coding region of a list of 20 genes. Differentially methylated regions were found for some of these genes. Virus-induced gene silencing (VIGS) of differentially methylated gene SlDET1 or SlPDS resulted in unusual brown pigmentation in Cnr fruits. These results suggest that comparative WGBS coupled with VIGS can be used to identify genes that may contribute to the colourless unripe phenotype of fruit in the Cnr epimutant.

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Acknowledgements

We thank Kenneth Manning for his initial involvement in this project and critical reading of this manuscript. We are grateful to David Baulcombe for his kind gift of the original PVX vector. This work was supported by Ministry of Agriculture of the People’s Republic of China, the National Transgenic Program of China (2016ZX08009001-004 to Yiguo Hong), National Natural Science Foundation of China (31370180 to Yiguo Hong, 31601765 to Weiwei Chen), Hangzhou Normal University Pandeng Program (201108 to Yiguo Hong), the Hangzhou City Government Innovative Program for Science Excellence (20131028 to Yiguo Hong), Zhejiang Provincial Natural Science Foundation (LY14C010005 to Nongnong Shi) and the UK Biotechnology and Biological Sciences Research Council (BBS/E/H/00YH0271 to Yiguo Hong).

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Correspondence to Yiguo Hong.

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Chen, W., Yu, Z., Kong, J. et al. Comparative WGBS identifies genes that influence non-ripe phenotype in tomato epimutant Colourless non-ripening. Sci. China Life Sci. 61, 244–252 (2018). https://doi.org/10.1007/s11427-017-9206-5

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Keywords

  • tomato Cnr
  • SlCMT3
  • SlDET1
  • SlPDS
  • DNA methylation
  • WGBS
  • VIGS