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通过人工智能和植物组学科学深入了解表观遗传记忆。

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

作者信息

Dobránszki Judit, Vassileva Valya, Agius Dolores R, Moschou Panagiotis Nikolaou, Gallusci Philippe, Berger Margot M J, Farkas Dóra, Basso Marcos Fernando, Martinelli Federico

机构信息

Centre for Agricultural Genomics and Biotechnology, University of Debrecen, PO Box 12., Nyíregyháza 4400, Hungary.

Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.

出版信息

J Integr Plant Biol. 2025 Sep;67(9):2320-2349. doi: 10.1111/jipb.13953. Epub 2025 Jun 24.


DOI:10.1111/jipb.13953
PMID:40552708
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.

摘要

植物展现出学习、交流、记忆以及形成依赖刺激的决策回路的非凡能力。与动物不同,植物的记忆独特地扎根于细胞、分子和生化网络,缺乏执行这些功能的专门器官。因此,植物能够有效地学习并应对各种挑战,适应反复出现的信号。人工智能(AI)和机器学习(ML)代表了生物科学的新前沿,有潜力预测气候变化相关环境胁迫下作物的行为。表观遗传机制作为植物记忆的基础蓝图,在调节植物对环境刺激的适应方面至关重要。它们通过调节染色质结构和可及性来实现这种适应,这有助于基因表达调控,并使植物能够动态适应不断变化的环境条件。在本综述中,我们描述了人工智能和机器学习中的新方法和途径,以阐明植物记忆如何响应环境刺激和引发机制。此外,我们探索利用跨代记忆进行植物育种的创新策略,以培育对多种胁迫具有抗性的作物。在此背景下,人工智能和机器学习有助于整合和分析植物应激反应的表观遗传数据,以优化亲本植物的培育。

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

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本文引用的文献

[1]
The Good, the Bad, and the Epigenetic: Stress-Induced Metabolite Regulation and Transgenerational Effects.

Epigenomes. 2025-3-29

[2]
Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection.

BMC Plant Biol. 2025-4-21

[3]
TransGeneSelector: using a transformer approach to mine key genes from small transcriptomic datasets in plant responses to various environments.

BMC Genomics. 2025-3-17

[4]
Interpretable deep learning of single-cell and epigenetic data reveals novel molecular insights in aging.

Sci Rep. 2025-2-11

[5]
Epitranscriptome profiles reveal participation of the RNA methyltransferase gene OsMTA1 in rice seed germination and salt stress response.

BMC Plant Biol. 2025-1-27

[6]
Grapevine cell response to carbon deficiency requires transcriptome and methylome reprogramming.

Hortic Res. 2024-9-28

[7]
A rare PRIMER cell state in plant immunity.

Nature. 2025-2

[8]
Epigenetic Mechanisms Driving Adaptation in Tropical and Subtropical Plants: Insights and Future Directions.

Plant Cell Environ. 2025-5

[9]
Disentangling genotype and environment specific latent features for improved trait prediction using a compositional autoencoder.

Front Plant Sci. 2024-12-16

[10]
RNA modifications in plant adaptation to abiotic stresses.

Plant Commun. 2025-2-10

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