1 Introduction

Tea, derived from the leaves of Camellia sinensis, is one of the most widely consumed non-alcoholic beverages globally. It holds tremendous economic importance, particularly in countries such as China, India, Kenya, and Sri Lanka, where tea production and export constitute a significant share of agricultural revenue. In addition to its economic value, tea is also recognized for its nutritional and health-promoting properties. Rich in antioxidants, amino acids, polyphenols, and caffeine, tea has been associated with numerous health benefits, including cardiovascular protection, anti-inflammatory effects, and cognitive enhancement (Wei et al., 2018).

Secondary metabolites in tea plants—such as catechins, theanine, caffeine, and volatile aromatic compounds—play a central role in defining tea's flavor, aroma, and mouthfeel. These metabolites are also key indicators of quality and are often used in the classification and valuation of tea products (Li et al., 2016). Beyond their contributions to sensory properties, many of these compounds are integral to the plant’s defense system. They help protect against herbivores, pathogens, and environmental stressors, thereby supporting the plant’s survival and fitness in diverse ecological niches.

It is essential for basic research and applied breeding work to understand how secondary metabolites are biosynthesized and regulated in tea plants. Their biosynthesis includes complex, multi-step enzymatic pathways with stringent controls at transcriptional, post-transcriptional, and epigenetic levels. Identification of important genes, enzymes, and regulatory networks provides a foundation for molecular breeding for improved quality, stress tolerance, and adaptation of tea (Wang et al., 2016; Liao et al., 2021). Further, advances in gene editing and multi-omics technologies open up possibilities for precision editing of metabolite profiles in tea cultivars.

The study provides a comprehensive overview of the recent advances in secondary metabolic pathways and their regulations in Camellia sinensis. It encapsulates the major secondary metabolites, biosynthetic pathways, and genetic and epigenetic regulations. By integrating multi-omics and functional studies, the review presents a shared framework to enhance an understanding of tea secondary metabolism. The acquired knowledge is important for onward basic plant science and has applied implications for molecular breeding for tea quality and stress tolerance enhancement, towards sustainable tea cultivation and industry development.

2 Major Secondary Metabolites in Tea Plants and Their Functions

2.1 Polyphenols

Polyphenols, especially catechins, flavonoids, theaflavins, and thearubigins, are the most abundant and significant bioactive compounds in tea. They contribute to the antioxidant, anti-inflammatory, anticancer, and cardiovascular protective effects of tea, and are key determinants of tea’s taste, color, and health benefits (Li et al., 2022).

2.2 Alkaloids

Alkaloids such as caffeine, theobromine, and theophylline are present in tea leaves. Caffeine is the most prominent, contributing to tea’s stimulating effects and bitterness, while also playing a role in plant defense against herbivores and pathogens (Kottawa-Arachchi et al., 2018).

2.3 Volatile aromatic compounds

Volatile compounds, including terpenoids, alcohols, aldehydes, and esters, are responsible for the characteristic aroma and flavor of tea. Key volatiles like linalool, geraniol, and methyl salicylate are crucial for tea quality and are influenced by both genetics and processing methods (Liu et al., 2024).

2.4 Amino acids and other functional compounds

Amino acids, particularly theanine, contribute to the umami taste and sweetness of tea. They also have calming effects and are important for the overall flavor profile and health benefits of tea (Kang et al., 2024). Other notable compounds include polysaccharides, vitamins, minerals, and saponins, which contribute to the nutritional value, immune regulation, and additional health-promoting properties of tea (Luo et al., 2023).

3 Elucidation of Secondary Metabolic Pathways

3.1 Phenylpropanoid pathway and flavonoid biosynthesis

Phenylpropanoid pathway is the central pathway in tea flavonoid biosynthesis, a group of compounds with primary importance to tea quality and resistance in plants. In plants, it is an enzyme cascade tightly controlled by transcription factors such as MYB, bHLH, and WD-repeat proteins. Recent transcriptomic research has discovered widespread gene expression and regulatory network differences among tea cultivars and identified AP2/ERF, WRKY, NAC, and MYB transcription factors to be involved in controlling both phenylpropanoid and flavonoid biosynthesis (Li et al., 2022). Flavonoid biosynthesis branches out into multiple sub-pathways to produce catechins, anthocyanins, and other compounds contributing to tea flavor and its health-promoting properties (Liu et al., 2021; Pratyusha and Sarada, 2022).

3.2 Terpenoid biosynthesis via MVA and MEP pathways

Terpenoids, responsible for much of tea’s aroma, are synthesized through the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways. Transcriptome data reveal that tea flowers accumulate higher levels of terpenoids than leaves, largely due to elevated expression of terpene synthase genes. The regulation of terpenoid biosynthesis differs between tissues, suggesting specialized control mechanisms in flowers versus leaves (Xia et al., 2017).

3.3 Purine metabolism and caffeine biosynthesis

Caffeine biosynthesis in tea plants proceeds via the purine alkaloid pathway, involving key enzymes such as S-adenosyl methionine synthase (SAMS), xanthosine methyltransferase (XMT), and caffeine synthase (TCS). Comparative transcriptomics between Camellia sinensis varieties have revealed that differences in caffeine and theobromine content are linked to the expression of these genes and their regulation by MYB and AP2/ERF transcription factors (Wang et al., 2025). The tea tree genome also shows lineage-specific expansions of caffeine biosynthetic genes, supporting the independent evolution of this pathway in tea.

3.4 Amino acid metabolism and theanine biosynthetic mechanism

Theanine is a unique amino acid in tea plants, which is primarily produced in the roots as an enzyme-catalyzed reaction between glutamic acid and ethylamine. It is catalyzed by theanine synthetase and is transported to the aerial parts of the plant produced as theanine. Both its biosynthesis and accumulation are controlled by environmental and transcriptional regulation, and a few MYB transcription factors participate in the process of regulation (Zhao et al., 2020). Similarly, catechins, being major secondary metabolites of tea plants, are biosynthesized through coordinated regulation of some significant structural genes and transcription factors. Experiments have shown that the catechin biosynthetic pathway is linked to gene expression and catalytic activity of genes such as CHS, CHI, F3H, F3′H, F3′5′H, DFR, ANS, LAR, ANR, and SCPL (Wei et al., 2018). These genes have tissue-specific expression modes, with higher expression levels in apical buds and young leaves, which are highly correlated with catechin accumulation. At the transcriptional level, co-expression network analysis has also demonstrated that various transcription factors (e.g., MYB and bHLH) are co-expressed with catechin biosynthetic genes, regulating their expression and metabolic processes in different tissues (Wei et al., 2018) (Figure 1). These findings reveal both the shared transcriptional processes and complex regulatory networks involved in the biosynthesis of secondary metabolites such as catechins and theanine in tea plants.

3.5 Precursors and branched pathways of aroma compound biosynthesis

Aroma compounds in tea are derived from multiple branched pathways, including those for terpenoids, phenylpropanoids, and amino acid derivatives. The expression of key biosynthetic genes and the interplay between different metabolic branches contribute to the diversity of volatile aromatic compounds in tea. Tissue-specific expression and developmental regulation further shape the aroma profile (Li et al., 2022).

4 Advances in Functional Genes and Key Enzymes

4.1 Cloning and expression regulation of structural genes

Recent studies have succeeded in cloning and isolating genes of structural genes involved in secondary metabolism, such as genes encoding phenylalanine ammonia-lyase (PAL), flavonoid 3′-hydroxylase (F3′H), and some MYB transcription factors. These genes are regulated by sophisticated networks of regulators such as transcription factors MYB, bHLH, and WD40, which respond to environmental triggers and developmental cues (Jiao et al., 2023). The establishment of gene co-expression databases and integrative transcriptomic profiling has enabled the detection of conserved gene modules and regulatory elements controlling secondary metabolic pathways in tea plants (Zhang et al., 2020).

4.2 Functional identification of key metabolic enzymes

Functional identification of key metabolic enzymes, such as those involved in proanthocyanidin and theanine biosynthesis, has been advanced through transient expression systems and recombinant protein assays. For example, subgroup 5 R2R3-MYB transcription factors have been shown to regulate proanthocyanidin biosynthesis, while specific MYB genes have been identified as regulators of theanine accumulation (Jiao et al., 2023). Transient transformation systems now allow for rapid gene function analysis and protein localization in tea leaves, accelerating the functional characterization of metabolic enzymes (Li et al., 2022).

4.3 Comparative analysis of varietal differences and expression patterns

Comparative transcriptomic and metabolomic analyses across different tea cultivars have revealed significant varietal differences in gene expression and metabolite accumulation. Weighted gene co-expression network analysis (WGCNA) and multi-omics approaches have identified key drivers of flavonoid variation and stress response, as well as the impact of natural and artificial selection on gene family expansion and functional divergence, such as in glycosyltransferase (UGT) genes (Wang et al., 2024). These findings provide valuable resources for breeding programs aimed at improving tea quality and stress tolerance.

5 Regulatory Mechanisms at Transcriptional and Epigenetic Levels

5.1 Roles of transcription factors in regulation

Transcription factors (TFs) like MYB, bHLH, WRKY, GRAS, and BZR1 families are key regulators of secondary metabolite biosynthesis in tea plants. MYB TFs, for instance, contribute to flavonoid, caffeine, theanine, and terpenoid biosynthesis, shoot development, and stress response (Li et al., 2022). BZR1 TFs are key factors in brassinosteroid signaling, integrating hormone and stress response, while WRKY and GRAS TFs play roles in abiotic stress resistance and developmental regulation. The TFs often act as components in complex regulatory networks, having responses to developmental and environmental cues in order to modulate the expression of metabolic genes.

5.2 Regulatory mechanisms involving non-coding RNAs

Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have emerged as important regulators of secondary metabolism in tea plants. They modulate the expression of key biosynthetic genes by acting as molecular sponges, forming competing endogenous RNA (ceRNA) networks, and targeting mRNAs for degradation or translational repression (Bordoloi et al., 2022). Recent studies have identified thousands of lncRNAs and miRNAs responsive to biotic and abiotic stresses, nitrogen application, and temperature, with many implicated in the regulation of catechin, theanine, and caffeine biosynthesis (Hu et al., 2023) (Figure 2).

5.3 Epigenetic modifications affecting metabolic gene expression

Alternative splicing and chromatin-level modifications add further complexity to the regulation of secondary metabolism. Full-length transcriptome analyses have revealed extensive alternative splicing events in key metabolic genes, suggesting that transcript diversity contributes to the fine-tuning of metabolite biosynthesis (Qiao et al., 2019). Although direct studies on DNA methylation and histone modifications in tea are limited, the presence of diverse transcript isoforms and regulatory lncRNAs points to a significant role for epigenetic mechanisms in metabolic gene expression (Qiao et al., 2019; Bordoloi et al., 2022).

5.4 Integration of hormone signaling in metabolic network regulation

Plant hormones such as abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), and strigolactones (SLs) interact with transcriptional and post-transcriptional regulators to modulate secondary metabolism. Hormone treatments alter the expression of key TFs and metabolic genes, affecting the accumulation of catechins, theanine, and caffeine. For example, strigolactones can reprogram transcriptional networks, influencing both secondary metabolite biosynthesis and nutrient signaling, while ABA has been shown to regulate theanine metabolism during postharvest withering.

6 Application of Multi-Omics Technologies in Secondary Metabolism Research

6.1 Combined transcriptomic and metabolomic analysis

Integrating transcriptomic and metabolomic data enables the mapping of gene expression to metabolite accumulation, revealing regulatory networks underlying secondary metabolite biosynthesis. This approach has clarified how polyphenol content changes during tea plant growth, development, and processing, and has identified candidate genes and pathways responsible for key metabolic traits (Li et al., 2022).

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 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.

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