Integrative Biology Journals
JIPB

J Integr Plant Biol. ›› 2026, Vol. 68 ›› Issue (2): 383-405.DOI: 10.1111/jipb.70066

• Metabolism and Biochemistry • Previous Articles     Next Articles

Light regulates tomato fruit metabolome via SlDML2-mediated global DNA demethylation

Zixin Zhang1,2†, Jing Zhang1,3†, Yi Wang1, Yuting Chen1, Qian Hu2, Xin Zhang1, Wen Li1, Yiren Xiao4,5, Ke Zhou6, Yanling Lai1, Dan Su1, Evangelos Tatsis4,5,7, Gaofeng Liu2, Mingchun Liu1, Zhenhui Zhong1 and Yang Zhang1*   

  1. 1. Key Laboratory of Bio‐resource and Eco‐environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
    2. College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
    3. College of Life Sciences, Shandong Agricultural University, Taian 271018, China
    4. National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 200032, China
    5. Chinese Academy of Sciences‐John Innes Center of Excellence for Plant and Microbial Science, Shanghai 200032, China
    6. Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops College of Horticulture, China Agricultural University, Beijing 100193, China
    7. School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China

    †These authors contributed equally to this work.
    *Correspondence: Yang Zhang (yang.zhang@scu.edu.cn)
  • Received:2025-08-16 Accepted:2025-09-18 Online:2025-10-23 Published:2026-02-02
  • Supported by:
    This work was supported by grants from the National Key Research and Development Program of China (2022YFF1001900), the National Natural Science Foundation of China (32200260), the Chengdu Agricultural Science and Technology Talent Cultivation Project (2023‐CD‐NYKJYC‐1), the Sichuan Science and Technology Program, China (2024NSFSC0036), the Institutional Research Fund of Sichuan University (2020SCUNL106) and the Fundamental Research Funds for the Central Universities (SCU2025D0003).

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Abstract: 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.

Key words: DNA demethylation, light signaling, SlDML2, SlHY5, tomato fruit

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