Light regulates tomato fruit metabolome via SlDML2‐mediated global DNA demethylation
Modifying the light formula is a central strategy for improving the yield and quality of fruits and vegetables in agriculture. While light signals have long been acknowledged as primary factors in regulating plant growth and development, their role in reprogramming metabolic networks is not well understood. Using tomato as a model, we demonstrate that supplementation with red or blue light induces metabolic shifts in tomato fruit. Through the creation of the Tomato Light-induced Expression Database (TomLED), we identified extensive transcriptomic and metabolic changes in tomato fruit under varying light conditions. Notably, the induction of key master regulators and metabolic genes is mediated by increased genome-wide DNA demethylation, facilitated by SlDML2. Additionally, we show that SlHY5, a central regulator in the light signaling pathway, directly induces the expression of SlDML2. This study reveals the molecular mechanisms by which light regulates the plant epigenome and establishes a direct link between light signals and plant metabolism.
Authors
- Ke Zhou (ORCID: https://orcid.org/0000-0001-5918-3735)
- Gaofeng Liu (ORCID: https://orcid.org/0000-0001-6238-7560)
- Evangelos C. Tatsis (ORCID: https://orcid.org/0000-0002-4013-1537)
- Yiren Xiao (ORCID: https://orcid.org/0000-0002-5252-328X)
- Zhenhui Zhong (ORCID: https://orcid.org/0000-0002-8438-0375)
- Wen Li (ORCID: https://orcid.org/0009-0000-8433-3141)
- Yi Wang (ORCID: https://orcid.org/0009-0007-2998-0865)
- Qian Hu (ORCID: https://orcid.org/0009-0000-6985-263X)
- Mingchun Liu (ORCID: https://orcid.org/0000-0001-8004-1758)
- Yang Zhang (ORCID: https://orcid.org/0000-0002-7793-1108)
- Zixin Zhang (ORCID: https://orcid.org/0000-0002-1135-6606)
- Yue Lai
- Jing Zhang (ORCID: https://orcid.org/0009-0009-6472-8432)
- Xin Zhang (ORCID: https://orcid.org/0009-0007-8595-6253)
- Yu-Ting Chen
- Dan Su (ORCID: https://orcid.org/0000-0002-6783-3758)
Institutions
- Southwest University (CN)
- Sichuan University (CN)
- Chengdu University (CN)
- Center for Excellence in Molecular Plant Sciences (CN)
- Sanya University (CN)
- China Agricultural University (CN)
- Shandong Agricultural University (CN)
Publication Details
- Journal
- Journal of Integrative Plant Biology
- Published
- 2025-10-23
- DOI
- https://doi.org/10.1111/jipb.70066
- Citations
- 3
- Primary Topic
- Light effects on plants
- Type
- article
- Field-Weighted Citation Impact
- 5.25
Funders
- National Natural Science Foundation of China
- China Agricultural University
- Sichuan University
- Southwest University
- National Key Research and Development Program of China
- Fundamental Research Funds for the Central Universities