Regulation of fruit development and ripening by DNA methylation

Recently, scientists from Shanxi Datong University and Chongqing University revealed that SlCMT4, which encodes a DNA methyltransferase responsible for de novo and non-CG methylation, plays an important role in diverse developmental processes of tomato. This study was published in Horticulture Research.

SlCMT4 (Solyc08g005400.2) was mutated in cv. ‘Ailsa Craig’ using the CRISPR/Cas9 system to confirm its function. Severe developmental defects were found in the SlCMT4 mutants, including small and thick leaves, increased lateral buds, defective stamens and pistils, small fruit size with reduced setting rate, and defective seed development. Alterations in hormone levels (IAA, tZR, strigol) were consistent with the multibranching phenotype of the SlCMT4 mutant plants. 

CRISPR-Cas9-mediated knockout of SlCMT4 induced the expression of two pollen-specific genes (PMEI and PRALF) that suppressed pollen wall development and pollen tube elongation, causing irregular and defective pollen. Transcriptome sequencing was used to study the transcript levels of tomato fruit ripening-related genes, and a number of ripening-related genes (such as PE1, PG2, and LOXB) were upregulated in the CR-08 mutant line.

Whole-genome bisulfite sequencing (WGBS) of fruits revealed that SlCMT4 knockout reduced genome-wide cytosine methylation, particularly CHH methylation. A reduction in methylation was also observed in a 2-kb region of the IMA and LOXB promoters in the SlCMT4-mutant fruits, indicating that the hypermethylation status of the CHH context was critical for the inhibition of IMA and LOXB promoter activity.

“This study clarified that SlCMT4 can cooperate in the epigenetic regulation of tomato fruit growth, development, and ripening by regulating the methylation patterns of key transcription factors,” the researchers said.

In brief, this study showed that SlCMT4 is required for normal development of tomato vegetative and reproductive organs.

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Reference

Authors

Xuhu Guo^1,2,*, Jianguo Zhao³, Zhiwen Chen³, Jun Qiao³, Yongfang Zhang¹, Hong Shen¹ and Zhongli Hu^4,*

Affiliation

1 School of Life Sciences, Shanxi Datong University, Datong 037009, China;

2 Protected Agricultural Technology Research and Development Center, Shanxi Datong University, Datong 037009, China;

3 Institute of Carbon Materials Science, Shanxi Datong University, Datong 037009, China;

4 Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400044, China

About Prof. Zhongli Hu

Prof. Zhongli Hu is currently a member of the Bioengineering College of Chongqing University. Both have been engaged in research on the molecular regulatory mechanisms of plant growth, development, and fruit ripening.