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Article|11 Feb 2019|OPEN
Diversity and redundancy of the ripening regulatory networks revealed by the fruitENCODE and the new CRISPR/Cas9 CNR and NOR mutants
Ying Gao1 , Ning Zhu2 , Xiaofang Zhu1 , Meng Wu1 , Jiang Cai-Zhong3,4 , Donald Grierson5 , Yunbo Luo1 , Wei Shen2 , Silin Zhong2 , and Da-Qi Fu1 , , Guiqin Qu,1 ,
1Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
2The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
3Department of Plant Sciences, University of California, Davis, CA 95616, USA
4Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA 95616, USA
5Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
*Corresponding author. E-mail: silin.zhong@cuhk.edu.hk,daqifu@cau.edu.cn,qugq@cau.edu.cn

Horticulture Research 6,
Article number: 39 (2019)
doi: https://doi.org/10.1038/s41438-019-0122-x
Views: 1198

Received: 05 Jan 2019
Revised: 18 Jan 2019
Accepted: 23 Jan 2019
Published online: 11 Feb 2019

Abstract

Tomato is considered as the genetic model for climacteric fruits, in which three major players control the fruit ripening process: ethylene, ripening transcription factors, and DNA methylation. The fruitENCODE project has now shown that there are multiple transcriptional circuits regulating fruit ripening in different species, and H3K27me3, instead of DNA methylation, plays a conserved role in restricting these ripening pathways. In addition, the function of the core tomato ripening transcription factors is now being questioned. We have employed CRISPR/Cas9 genome editing to mutate the SBP-CNR and NAC-NOR transcription factors, both of which are considered as master regulators in the current tomato ripening model. These plants only displayed delayed or partial non-ripening phenotypes, distinct from the original mutant plants, which categorically failed to ripen, suggesting that they might be gain-of-function mutants. Besides increased DNA methylation genome-wide, the original mutants also have hyper-H3K27me3 in ripening gene loci such as ACS2, RIN, and TDR4. It is most likely that multiple genetic and epigenetic factors have contributed to their strong non-ripening phenotypes. Hence, we propose that the field should move beyond these linear and two-dimensional models and embrace the fact that important biological processes such as ripening are often regulated by highly redundant network with inputs from multiple levels.