Plant Gene and Trait 2025, Vol.16, No.5, 225-233 http://genbreedpublisher.com/index.php/pgt 230 higher than that of the traditional extraction method (Wang et al., 2019; Qiu et al., 2024; Zhang et al., 2024). In addition, synthetic biology can not only efficiently produce natural saponins, but also synthesize non-natural saponins with novel structures and potential medicinal value through enzyme engineering and substrate modification (Dai et al., 2018; Shi et al., 2021). In terms of industrial application, microbial cell factories have provided a foundation for the industrialization of saponins due to their advantages such as low cost, sustainability and scalability. The development of high-yield systems and new saponins has opened up broad application prospects in fields such as medicine, health products and functional foods (Li et al., 2022b; Yao et al., 2022; Qiu and Blank, 2023; Son et al., 2024; Qiu and Blank, 2025). 7 Challenges and Research Gaps 7.1 Complexity of multi-gene biosynthetic pathways The synthesis of active substances such as ginsenosides relies on many genes and complex metabolic networks. The genome of ginseng is large and there are many repetitive sequences. The families of related enzymes (such as UDP-glycosyltransferases and P450 enzymes) have a large number of members and significant functional differences. Therefore, it is very difficult to identify the key genes and reconstruct them in heterologous systems (Yang et al., 2018; Chopra et al., 2021). In addition, the expression levels of different enzymes, substrate selectivity and activity will all affect product accumulation. Bottleneck and bypass metabolisms in the pathway also make synthetic design more complex (Li et al., 2022a; Yao et al., 2022; Zhang et al., 2022). 7.2 Technical difficulties in stable transformation of P. ginseng Ginseng itself is not easy to undergo genetic transformation. A stable transgenic system is difficult to establish, with low transformation efficiency and a long regeneration cycle. Although in vitro culture systems such as hairy roots and callus can be used for gene function verification and metabolic studies, there are still many limitations at the whole-plant level, such as strong genotype dependence, harsh culture conditions, and low regeneration rate (Zou et al., 2021; Xu et al., 2023; Zhu et al., 2024). Meanwhile, whether the expression of exogenous genes is stable and whether the copy number is controllable will also affect the accumulation of target metabolites (Yao et al., 2020). 7.3 Regulatory and biosafety considerations in synthetic biology applications The application of synthetic biology in medicinal plants like ginseng often requires gene editing, the introduction of exogenous genes and the construction of microbial factories. However, these operations are subject to strict supervision and safety assessment. At present, there are no unified standards for the food and drug safety, environmental release risks and ethical issues of genetically modified ginseng and its metabolites, which limits industrialization (Yang et al., 2018; Chopra et al., 2021). In addition, the production of high-value products such as ginsenosides in microbial systems also involves issues of intellectual property rights, product traceability and market access, which also need to be further regulated (Li et al., 2022a; Zhang et al., 2022). 8 Future Perspectives 8.1 Integration of AI, machine learning, and computational modeling for pathway design With the in-depth research on the ginseng genome and metabolic network, artificial intelligence (AI), machine learning (ML), and computational modeling have begun to play a significant role in synthetic biology. AI and ML can predict key enzymes and regulatory elements by analyzing large-scale omics data and infer their effects on metabolic flow, thereby helping to optimize the synthetic pathways of functional components such as ginsenosides (Kim et al., 2018). Modeling methods based on genomes and transcriptomes can also reconstruct complex metabolic pathways and identify appropriate regulatory targets, providing theoretical support for the efficient synthesis of novel or high-content saponins (Song et al., 2024). In the future, combining the automated design of AI with high-throughput experiments is expected to significantly accelerate the directional modification of functional metabolites of ginseng and the breeding of new varieties. 8.2 Synthetic consortia and bioreactor systems for large-scale metabolite production In the field of metabolic engineering, synthetic biology has driven the development of microbial cell factories. Saccharomyces cerevisiae and engineered bacteria are often used as hosts. Through multi-enzyme co-expression
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