J Integr Plant Biol ›› 2025, Vol. 67 ›› Issue (9): 2320-2349.DOI: 10.1111/jipb.13953

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  • 收稿日期:2025-02-08 接受日期:2025-05-20 出版日期:2025-09-01 发布日期:2025-09-02

Gaining insights into epigenetic memories through artificial intelligence and omics science in plants

Judit Dobránszki1*, Valya Vassileva2*, Dolores R. Agius3, Panagiotis Nikolaou Moschou4,5,6, Philippe Gallusci7, Margot M.J. Berger7, Dóra Farkas1, Marcos Fernando Basso8 and Federico Martinelli8*   

  1. 1. Centre for Agricultural Genomics and Biotechnology, University of Debrecen, PO Box 12., Nyíregyháza 4400, Hungary
    2. Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
    3. Department of Biology, Ġ.F. Abela Junior College, Ġuzè Debono Square, Msida MSD 1252, Malta
    4. Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
    5. Department of Biology, University of Crete, Heraklion 71500, Greece
    6. Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology‐Hellas, Heraklion 71500, Greece
    7. UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), University of Bordeaux, Bordeaux Sciences Agro, Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut des Sciences de la Vigne et du Vin (ISVV), Villenave d'Ornon 33882, France
    8. Department of Biology, University of Florence, Firenze 50019, Italy

    *Correspondences: Judit Dobránszki (dobranszki@freemail.hu); Federico Martinelli (federico.martinelli@unifi.it); Valya Vassileva (valyavassileva@bio21.bas.bg, Dr. Vassileva is fully responsible for the distribution of all materials associated with this article)
  • Received:2025-02-08 Accepted:2025-05-20 Online:2025-09-01 Published:2025-09-02

Abstract: Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus-dependent decision-making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs for these functions. Consequently, plants can effectively learn and respond to diverse challenges, becoming used to recurring signals. Artificial intelligence (AI) and machine learning (ML) represent the new frontiers of biological sciences, offering the potential to predict crop behavior under environmental stresses associated with climate change. Epigenetic mechanisms, serving as the foundational blueprints of plant memory, are crucial in regulating plant adaptation to environmental stimuli. They achieve this adaptation by modulating chromatin structure and accessibility, which contribute to gene expression regulation and allow plants to adapt dynamically to changing environmental conditions. In this review, we describe novel methods and approaches in AI and ML to elucidate how plant memory occurs in response to environmental stimuli and priming mechanisms. Furthermore, we explore innovative strategies exploiting transgenerational memory for plant breeding to develop crops resilient to multiple stresses. In this context, AI and ML can aid in integrating and analyzing epigenetic data of plant stress responses to optimize the training of the parental plants.

Key words: deep learning, DNA methylation, gene expression, machine learning, stress memory, transgenerational inheritance

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