Journal of Tea Science Research, 2024, Vol.14, No.6, 313-321 http://hortherbpublisher.com/index.php/jtsr 319 flavonoid and theanine biosynthetic pathways. The intricate roles played by MYB transcription factors and other regulatory proteins have been unraveled, showing their central role in regulating shoot development, stress tolerance, and biosynthesis of important secondary metabolites. Alternative splicing and non-coding RNAs have appeared as important regulatory layers, playing a role in the transcriptomic and post-transcriptional complexity underlying metabolite diversity. Multi-omics and network analysis have identified the hub genes and co-expression modules that are involved in biosynthesis of catechins, theanine, and caffeine and have pointed to the influence of environmental factors such as light and nutrient status. Single-cell and tissue-specific studies have further elucidated the influence of spatial regulation, particularly of root-specific theanine metabolism. Despite these advances, several limitations persist. Many biosynthetic and regulatory pathways remain incompletely characterized, especially for less abundant or novel metabolites. The integration of multi-omics data into predictive, systems-level models is still in its early stages, and functional validation of candidate genes and regulatory elements lags behind discovery. The influence of environmental and microbial factors on secondary metabolism is not fully understood, and translating molecular insights into practical breeding strategies for high-quality, resilient tea cultivars remains a significant challenge. In the years to come, multi-omics, systems biology, and molecular breeding platforms together have the potential for the tea sector. Integrative application of the omics will facilitate a full understanding of secondary metabolism, whereas systems biology approaches can identify key regulative nodes to manage for directed manipulation. Molecular breeding as marker-assisted selection and genome editing can speed up the development of tea cultivars with better quality and stress tolerance. These innovations will enable sustainable industry development by being able to sustain precision breeding and cultivation operations that optimize metabolite content profiles and confer resistance to environmental variation and ultimately enable production of high-quality tea. Acknowledgments The authors sincerely thank Ms. Li for her invaluable assistance in compiling literature and supporting the completion of this manuscript. Additionally, heartfelt gratitude is extended to the two anonymous peer reviewers for their comprehensive evaluation of the manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. Reference Baysoy A., Bai Z., Satija R., and Fan R., 2023, The technological landscape and applications of single-cell multi-omics, Nature Reviews Molecular Cell Biology, 24(10): 695-713. https://doi.org/10.1038/s41580-023-00615-w Bordoloi K., Baruah P., Tanti B., Gill S., and Agarwala N., 2022, Helopeltis theivora-responsive transcriptomic reprogramming uncovers long non-coding RNAs as possible regulators of primary and secondary metabolism in tea plant, Journal of Plant Growth Regulation, 42: 6523-6548. https://doi.org/10.1007/s00344-022-10893-x Hasan N., Choudhary S., Naaz N., Sharma N., and Laskar R., 2021, Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes, Journal of Genetic Engineering and Biotechnology, 19: 132. https://doi.org/10.1186/s43141-021-00231-1 Hu S., Hu Y., Mei H., Li J., Xuan W., Jeyaraj A., Zhao Z., Zhao Y., Han R., Chen X., and Li X., 2023, Genome-wide analysis of long non-coding RNAs (lncRNAs) in tea plants (Camellia sinensis) lateral roots in response to nitrogen application, Frontiers in Plant Science, 14: 1080427. https://doi.org/10.3389/fpls.2023.1080427 Jiao T., Huang Y., Wu Y., Jiang T., Li T., Liu Y., Liu Y., Han Y., Liu Y., Jiang X., Gao L., and Xia T., 2023, Functional diversity of subgroup 5 R2R3-MYBs promoting proanthocyanidin biosynthesis and their key residues and motifs in tea plant, Horticulture Research, 10: uhad135. https://doi.org/10.1093/hr/uhad135 Kang S., Lee S., Kwon Y., Moon D., Sun J., Hwang K., and Moon J., 2024, Characteristic of phenotype, amino acids and volatile compounds for fresh tea leaves of Korean tea cultivars (Camellia sinensis (L.) O. Kuntze), Applied Biological Chemistry, 67: 1-16. https://doi.org/10.1186/s13765-024-00919-1
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