Journal of Tea Science Research, 2024, Vol.14, No.6, 313-321 http://hortherbpublisher.com/index.php/jtsr 318 6.2 Proteomic and epigenomic insights into metabolic pathways Proteomics, especially mass spectrometry-based methods, provides dynamic snapshots of protein abundance and post-translational modification that complement transcriptomic and metabolomic data. Together with epigenomic investigations, these approaches provide a comprehensive view of how gene regulation, protein function, and chromatin state collectively shape metabolic pathways in plants (Rajczewski et al., 2022; Sanches et al., 2024). Such integration is necessary to comprehend the complexity of secondary metabolism at more than the gene expression level. 6.3 Temporal-spatial expression profiling and environmental response studies Single-cell and spatial multi-omics technologies allow for the dissection of temporal and spatial patterns of gene and metabolite expression. These methods have been used to profile how secondary metabolism responds to environmental cues, developmental stages, and tissue-specific factors, providing insights into the regulation and localization of metabolic processes (Baysoy et al., 2023; Vandereyken et al., 2023). 6.4 Case study: Integrated omics revealing the accumulation patterns of tea polyphenols A multi-omics approach combining genomics, transcriptomics, proteomics, and metabolomics has been applied to study tea polyphenol formation and transformation. This has enabled the identification of key regulatory genes, enzymes, and environmental factors influencing polyphenol accumulation, and has provided a roadmap for improving tea quality through targeted breeding and processing strategies (Li et al., 2022). 7 Potential Applications and Challenges in Tea Secondary Metabolism Research 7.1 Application of marker-assisted selection (MAS) in elite germplasm screening MAS has revolutionized tea breeding by enabling precise identification and selection of desirable traits, such as disease resistance, nitrogen use efficiency, and quality-related metabolites. The development of SNP, KASP, and ILP markers, as well as high-quality reference genomes, has accelerated elite germplasm screening and variety identification in tea (Li et al., 2023; Shen et al., 2024). MAS is now integral for improving traits like yield, stress tolerance, and flavor in tea breeding programs (Hasan et al., 2021). 7.2 Frontiers in gene editing and synthetic biology for functional compound regulation Gene editing technologies, especially CRISPR/Cas9, are emerging as powerful tools for functional validation and precise modification of genes controlling secondary metabolism. These approaches enable targeted improvement of traits such as polyphenol content, disease resistance, and stress adaptation, and hold promise for synthetic biology applications to engineer novel or enhanced functional compounds in tea (Thomson et al., 2022). 7.3 Exploration of nutritional enhancement and high-value utilization of tea products Advances in genomics and molecular breeding facilitate the development of tea varieties with enhanced nutritional profiles, such as increased polyphenols, amino acids, and health-promoting compounds. Marker-assisted and genomic selection approaches support the creation of high-value tea products tailored for specific health benefits and market demands (Zhou et al., 2025). 7.4 Current research bottlenecks and the need for interdisciplinary collaboration Despite these advances, challenges remain, including the complexity of polygenic traits, limited functional validation of candidate genes, and the integration of omics data into breeding pipelines. Addressing these bottlenecks requires interdisciplinary collaboration among geneticists, molecular biologists, breeders, and data scientists to translate molecular insights into practical breeding outcomes (Hasan et al., 2021; Li et al., 2023). 8 Concluding Remarks The last few years have witnessed tremendous advancements in unravelling secondary metabolism and its regulation in tea plants. Multi-omics approaches have deciphered the dynamic, complex regulation of key metabolites such as flavonoids, theanine, and caffeine that form the foundation of tea quality and nutritional content. Dynamic DNA methylation, for example, has been elucidated to be crucial for mediating seasonally dependent regulation of accumulation in secondary metabolites and directly impacting the expression of genes for
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