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Unlocking gene regulatory networks for crop resilience and sustainable agriculture

Nature Biotechnology volume 43, pages 1254–1265 (2025)Cite this article

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Abstract

Understanding the complex mechanisms of gene regulatory networks (GRNs) has emerged as a transformative approach in agricultural research. By deciphering the regulatory mechanisms underlying key traits, GRN studies offer opportunities to enhance crop resilience to environmental challenges, improve yield and ensure sustainable food production. In this Review, we highlight the importance of GRN research in agriculture and explore how cutting-edge biotechnology, interdisciplinary approaches and computational modeling techniques are addressing the challenges in the field. We discuss how integrating diverse datasets at different resolutions empowers us to unravel the complex genetic networks governing crop responses to climate change, pests and diseases. By harnessing the power of GRNs, we have the potential to transform crop improvement strategies, develop stress-tolerant varieties and ensure global food security. We provide insights into the current opportunities and challenges of GRN research in agriculture, bridging the gap between scientific advancements and the pressing need for sustainable agricultural practices.

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Fig. 1: Leveraging GRN analysis for agricultural challenges.
Fig. 2: Integrating multiomics data for GRN inference.
Fig. 3: From biological challenges to GRN inference and genetic engineering applications.

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Acknowledgements

We extend our gratitude to H. Pai for valuable discussions and insights regarding figure design. Research support for R.L., B.S.B. and P.D. was generously provided by the European Union’s Horizon Europe program through the European Research Council Starting Grant (ERC-2021-StG) R-ELEVATION (grant no. 101039824). Additionally, X.H. acknowledges funding support from the Luxembourg National Research Fund (FNR) through the DTU Grant (grant no. 11012546). Due to word count limitations, we apologize to the authors of those relevant works that could not be cited in this Review. The omission of any research or publications is unintentional and does not diminish their importance or contribution to the field. We acknowledge and appreciate the extensive body of work that has been carried out by researchers in this field.

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Author notes

  1. These authors contributed equally: Richalynn Leong, Xin He, Bob Sebastiaan Beijen.

Authors and Affiliations

  1. Institute of Biology Leiden, Leiden University, Leiden, the Netherlands

    Richalynn Leong, Bob Sebastiaan Beijen & Pingtao Ding

  2. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg

    Xin He & Jorge Goncalves

  3. School of Artificial Intelligence, Changchun University of Science and Technology, Jilin, China

    Xin He

  4. Crop Evolution Laboratory, Kyoto University, Muko, Japan

    Toshiyuki Sakai

  5. Department of Plant Sciences, University of Cambridge, Cambridge, UK

    Jorge Goncalves

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P.D. established the framework of the Review. All authors contributed to writing and editing the manuscript.

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Correspondence to Pingtao Ding.

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Leong, R., He, X., Beijen, B.S. et al. Unlocking gene regulatory networks for crop resilience and sustainable agriculture. Nat Biotechnol 43, 1254–1265 (2025). https://doi.org/10.1038/s41587-025-02727-4

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