Journal of Energy Bioscience 2024, Vol.15, No.6, 378-387 http://bioscipublisher.com/index.php/jeb 386 Future research should focus on the following directions: (1) Integrate single-cell sequencing and spatial metabolomics technology to dynamically analyze the spatiotemporal specificity of isoflavone synthesis units during organ development; (2) Construct a mathematical model of metabolic network to simulate the laws of metabolic flux reprogramming under environmental disturbances and establish a precise and controllable genetic regulation strategy; (3) Develop a modular metabolic system based on synthetic biology to reduce bypass metabolic interference through compartmentalization engineering; (4) Combine intelligent agricultural equipment to establish a phenotype group-environment group association model and optimize cultivation management plans to stabilize the output of secondary metabolites. At the application level, the bioavailability and product stability of isoflavones can be improved through food processing technology innovations such as directed fermentation. Breakthroughs in these research directions will promote the actual transformation of isoflavones from basic research to agricultural quality improvement and functional food development. Acknowledgments Sincere thanks to every member of the project team for their hard work and sincere cooperation, as well as the valuable opinions and careful guidance of the reviewers, which have made this article perfect. Conflict of Interest Disclosure The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. 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