1 Introduction

Flavonoids are among the most abundant and functionally significant secondary metabolites in Camellia sinensis (tea plant). These polyphenolic compounds are integral to the quality and physiological attributes of tea leaves, contributing to coloration (such as the purple hue in anthocyanin-rich cultivars), bitterness, astringency, and antioxidant capacity. Catechins, the dominant flavonoids in tea, are directly associated with the health-promoting effects of green tea, while other subclasses like flavonols and anthocyanins influence both sensory characteristics and adaptive responses to environmental stimuli. In planta, flavonoids serve as essential agents in UV protection, pathogen resistance, and stress mitigation, underscoring their biological and ecological importance in tea cultivation (Li et al., 2022).

Beyond their role in plant physiology, tea flavonoids offer a wide range of nutritional and therapeutic benefits to humans. Extensive research has demonstrated their antioxidant, anti-inflammatory, cardioprotective, neuroprotective, and anticancer properties. Catechins such as epigallocatechin gallate (EGCG) have been particularly well-studied for their ability to scavenge free radicals, modulate cell signaling pathways, and influence metabolic health. The regular consumption of flavonoid-rich tea has been linked to reduced risks of chronic diseases, including cardiovascular disease, obesity, and certain cancers, making them key functional compounds in human nutrition and preventive medicine (Wang et al., 2021; Lv et al., 2022).

Because of their central roles in both human and plant health, clarification of the biosynthetic and regulatory mechanisms of flavonoids in tea plants has great interest. The flavonoid biosynthetic pathway is complex with multiple branches originated from the phenylpropanoid pathway and tightly controlled by networks of structural genes, transcription factors, and post-transcriptional regulators. The recent advances in genomics, transcriptomics, and metabolomics have enabled the identification of key genes and regulatory factors, yet the general knowledge of how these networks are controlled—especially under environmental and developmental cues—is still absent. Such a knowledge gap needs to be filled for the genetic improvement of tea cultivars through molecular breeding (Wang et al., 2018).

This study outlines the recent advances in the genetic and molecular control of flavonoid biosynthesis in Camellia sinensis. It includes the principal classes of tea flavonoids, the involved biosynthetic pathways, the functions of structural genes and transcriptional regulators, and epigenetic and non-coding RNA-mediated regulation. Besides, it highlights the application of multi-omics approaches in flavonoid network dissection and explores the prospects of these discoveries in molecular breeding and functional tea product development. By the integration of existing knowledge, this study is supposed to facilitate future research and innovation in tea quality and plant metabolic engineering.

2 Overview of Flavonoid Types and Biosynthetic Pathways in Tea Plants

2.1 Major types of flavonoids: catechins, anthocyanins, flavonols, etc.

Tea plants synthesize a diverse array of flavonoids, with catechins (such as epigallocatechin gallate, EGCG), anthocyanins, and flavonols (like quercetin and kaempferol derivatives) being the most prominent. Catechins are especially abundant in young leaves and are key contributors to tea’s taste, color, and health benefits. Anthocyanins are responsible for the purple coloration in certain tea cultivars, while flavonols are widely distributed and contribute to both color and antioxidant properties. Flavonoid glycosides, such as 7-O-neohesperidoside, also play a role in bitterness and astringency (Song et al., 2022).

2.2 Core biosynthetic pathways: phenylpropanoid pathway and flavonoid-specific branches

Flavonoid biosynthesis in tea plants is activated by the phenylpropanoid pathway, in which cinnamic acid is formed from phenylalanine by phenylalanine ammonia-lyase (PAL). This is succeeded by a series of enzyme-catalyzed reactions by chalcone synthase (CHS), chalcone isomerase (CHI), and flavanone 3-hydroxylase (F3H) that leads to the production of various flavonoid subclasses. Branch pathways produce particular metabolites such as catechins, anthocyanins, and flavonols each regulated by particular enzymes and transcription factors. Recent research emphasizes the function of gene duplication (e.g., CHS genes), protein complexes, and post-translational modifications in regulating pathway efficiency and diversity (Shen et al., 2022).

2.3 Tissue-specific and spatiotemporal expression patterns of flavonoid biosynthesis

Flavonoid biosynthesis in tea plants is highly tissue- and stage-specific. Young leaves and buds accumulate the highest levels of catechins and flavan-3-ols, while anthocyanins and certain flavonols are enriched in purple leaves or at specific developmental stages. The expression of biosynthetic genes and regulatory factors varies across tissues and in response to environmental cues such as light, nitrogen, and sugar signals, reflecting complex spatiotemporal regulation. For example, UV-B light and sugar signals can upregulate key biosynthetic genes, while nitrogen deficiency can enhance flavonoid accumulation in roots (Wang et al., 2021; Song et al., 2022; Li et al., 2024) (Figure 1).

3 Key Structural Genes Involved in Flavonoid Biosynthesis

3.1 Genes encoding key enzymes in the phenylpropanoid pathway: PAL, C4H, 4CL

Phenylpropanoid pathway is the pathway that regulates the initiation of flavonoid biosynthesis. The conversion of phenylalanine to cinnamic acid is catalyzed by phenylalanine ammonia-lyase (PAL), followed by cinnamate 4-hydroxylase (C4H) and 4-coumarate:CoA ligase (4CL) to form 4-coumaroyl-CoA, a major precursor in flavonoid biosynthesis. There are various PAL and 4CL genes in Camellia sinensis plants, such as Cs4CL1 and Cs4CL2, which have tissue-specific expression and varied responses to environmental stimuli such as UV-B and wounding (Li et al., 2022).

3.2 Structural genes in the flavonoid pathway: CHS, CHI, F3H, DFR, ANS

Chalcone synthase (CHS) catalyzes the first committed step in flavonoid biosynthesis, producing chalcones from 4-coumaroyl-CoA. Chalcone isomerase (CHI) isomerizes chalcones to flavanones, which are hydroxylated by flavanone 3-hydroxylase (F3H) to dihydroflavonols. Dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) act on these intermediates to form anthocyanidins and other flavonoids. Tea plants contain multiple CHS genes, wherein gene duplication incidents have influenced functional diversity and environmental responsiveness, such as UV-B-induced expression. Functional confirmation has determined CsCHS, CsCHI, CsDFR, and CsANS functions in flavonoid biosynthesis (Wu et al., 2020).

3.3 Downstream modification-related genes: UGTs, LAR, ANR, etc.

Downstream modifications diversify flavonoid structures. UDP-glycosyltransferases (UGTs) catalyze glycosylation, affecting solubility and taste. In tea, CsUGT75L12 and CsUGT79B28 are responsible for sequential glucosylation and rhamnosylation, producing bitter flavonoid 7-O-neohesperidoside (Dai et al., 2022). Leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) are involved in the biosynthesis of catechins and proanthocyanidins, with their expression correlating with flavonoid accumulation in different tissues and cultivars (Wang et al., 2018).

3.4 Advances in expression profiling and functional validation of key genes

Recent advances include genome-wide identification, transcriptome analysis, and functional validation of flavonoid biosynthetic genes. Co-expression and association studies have revealed that structural genes and transcription factors (e.g., MYB, bHLH) exhibit specific expression patterns during leaf development and in response to environmental cues (Zhu et al., 2020). Functional assays, such as gene overexpression and complementation in model plants, have confirmed the roles of key genes like CHS, UGTs, and 4CL in flavonoid biosynthesis and modification (Dai et al., 2022; Li et al., 2022).

4 Transcription Factor Networks Regulating Flavonoid Biosynthesis

4.1 Dominant role of the MYB family of transcription factors

The MYB family plays a central and diverse role in regulating flavonoid biosynthesis in tea plants. Specific MYB transcription factors, such as CsMYB2, CsMYB8, CsMYB23, CsMYB26, CsMYB67, and CsMYB99, have been shown to control the expression of structural genes involved in the biosynthesis of catechins, anthocyanins, and flavonols. These MYBs also participate in shoot development, stress responses, and the regulation of other secondary metabolites, highlighting their functional diversity and importance in tea quality and adaptation (Figure 2) (Li et al., 2022; Chen et al., 2025).

4.2 Coordinated regulation by bHLH and WD40 proteins

bHLH and WD40 proteins act as co-regulators with MYB transcription factors. bHLH proteins (such as CsbHLH and bHLH96) interact with MYBs to modulate the expression of flavonoid biosynthetic genes, while WD40 proteins (like CsTTG1) serve as scaffolds, stabilizing the transcriptional complexes. These interactions are crucial for the precise regulation of flavonoid pathway genes and for tissue- and stage-specific flavonoid accumulation (Wang et al., 2018; Zhu et al., 2020).

4.3 Molecular model of the MYB-bHLH-WD40 (MBW) transcriptional complex

The MBW complex, composed of MYB, bHLH, and WD40 proteins, is a well-established regulatory module in flavonoid biosynthesis. In tea plants, this complex directly activates the transcription of key structural genes such as ANS, FLS, and UFGT, thereby controlling the biosynthesis of anthocyanins and other flavonoids. Functional studies have demonstrated that the co-expression of MYB and WD40 proteins enhances the transcription of target genes, confirming the cooperative nature of the MBW complex (Wang et al., 2018; Ye et al., 2023).

4.4 Functional diversity and genotype-specific regulation of transcription factors

Flavonoid biosynthesis transcription factors are also extremely functionally diverse and regulated by genotype. For example, expression and functions of the MYB and bHLH factors could vary among tea cultivars, and these variations lead to differences in flavonoid content and composition. Environmental factors such as light, temperature, and hormone signals also modulate the activity of the transcription factors to ultimately lead to dynamic and context-dependent flavonoid biosynthesis regulation (Song et al., 2022).

5 Epigenetic Regulation and the Role of Non-coding RNAs

5.1 Influence of DNA methylation and histone modifications on gene expression

Epigenetic mechanisms such as DNA methylation and histone modifications play a crucial role in regulating gene expression in plant secondary metabolism, including flavonoid biosynthesis. These modifications can alter chromatin structure, thereby activating or repressing the transcription of key biosynthetic genes. Although direct studies in tea plants are limited, evidence from broader plant research indicates that epigenetic regulation is a key layer of control in the biosynthesis of flavonoids and other secondary metabolites (Li et al., 2022).

5.2 Emerging roles of miRNAs and lncRNAs in flavonoid pathway regulation

MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are being increasingly recognized as key flavonoid biosynthesis regulators. miRNAs may regulate structural genes and transcription factors, such as those within the MYB-bHLH-WD40 complex, by translational repression or cleavage of mRNAs. For example, it has been shown that miRNAs can regulate structural genes and regulatory proteins to modulate flavonoid accumulation and how plants respond to the environment (Yang et al., 2021). 

lncRNAs can work as transcriptional, post-transcriptional, and epigenetic regulators. Recent studies in plants such as Ginkgo biloba have identified lncRNAs that regulate flavonoid biosynthesis by acting either as precursors or as decoys of miRNAs, or directly influencing the expression of biosynthetic genes. Individual lncRNAs (such as lnc10 and lnc11) overexpression has been shown to promote flavonoid content and modulate related genes in transgenic plants (Liu et al., 2020; Li et al., 2023).

5.3 Interaction models between epigenetic and transcriptional regulation

There is growing evidence that epigenetic modifications and non-coding RNAs interact with classical transcriptional regulatory networks. miRNAs and lncRNAs can modulate the activity of transcription factors, while epigenetic marks can influence the accessibility of DNA to these factors. This multi-layered regulation enables plants to finely tune flavonoid biosynthesis in response to developmental and environmental signals, integrating epigenetic, transcriptional, and post-transcriptional controls into a complex regulatory network (Yang et al., 2021).

6 Applications of Multi-Omics Approaches in Flavonoid Research

6.1 Genomics and transcriptomics for key gene discovery

Genomics and transcriptomics enable identification of genes and regulatory elements controlling flavonoid biosynthesis. High-throughput sequencing and transcriptome profiling yield gene expression profiles, unveiling candidate genes and transcription factors modulating flavonoid pathways. These approaches are pivotal to mapping biosynthetic networks and understanding genetic variation underlying flavonoid diversity (Subramanian et al., 2020; Wörheide et al., 2021).

6.2 Integration of metabolomics and proteomics to reveal metabolic flow and regulation points

Metabolomics provides a comprehensive profile of flavonoid compounds, while proteomics identifies and quantifies enzymes and regulatory proteins. Integrating these datasets allows researchers to trace metabolic flux, pinpoint regulatory bottlenecks, and link gene expression to metabolite accumulation. For example, multi-omics analysis in genetically engineered plants has shown how flavonoid accumulation can impact precursor availability and alter cellular metabolism (Meng et al., 2020; Wörheide et al., 2021).

6.3 Multi-omics integration for network modeling and function prediction

Combining genomics, transcriptomics, proteomics, and metabolomics enables the construction of detailed molecular networks. Advanced integration methods, including data-driven and knowledge-based approaches, facilitate the prediction of gene function, regulatory interactions, and pathway dynamics. These models help identify key regulatory nodes and potential targets for metabolic engineering (Subramanian et al., 2020; Vandereyken et al., 2023).

6.4 Case studies: Omics-driven insights into differential flavonoid accumulation

Case studies using multi-omics approaches have provided insights into the mechanisms underlying differential flavonoid accumulation. For instance, integrated omics analysis in transgenic tomato revealed that increased flavonoid production can deplete precursor pools and affect other metabolic pathways, highlighting the interconnectedness of metabolic networks (Meng et al., 2020). Such studies demonstrate the power of multi-omics to uncover complex regulatory relationships and guide targeted interventions.

7 Molecular Breeding and Applied Prospects

7.1 Development of QTLs and molecular markers related to flavonoids

Advances in genomics and transcriptomics have enabled the identification of quantitative trait loci (QTLs) and molecular markers associated with flavonoid content and composition. These tools facilitate marker-assisted selection and accelerate breeding for high-flavonoid cultivars. The integration of omics data has improved the mapping of genetic regions influencing flavonoid biosynthesis, supporting the development of new varieties with enhanced nutritional and functional properties (D’Amelia et al., 2018; Zhang et al., 2019).

7.2 Potential of gene editing (e.g., CRISPR) in quality trait improvement

Gene editing technologies, such as CRISPR/Cas9, offer precise tools for modifying key genes in flavonoid biosynthetic pathways. These approaches enable targeted enhancement or suppression of specific flavonoid compounds, improving plant quality traits, stress tolerance, and health benefits. Synthetic biology and metabolic engineering further expand the potential for producing novel or high-value flavonoids in both plants and microbial systems (Nabavi et al., 2018; Wang et al., 2024).

7.3 Targeted breeding strategies for functional tea product development

Targeted breeding strategies, informed by molecular markers and functional genomics, allow for the development of tea cultivars with tailored flavonoid profiles. These strategies support the creation of functional tea products with specific health benefits, improved taste, and enhanced stress resilience. The use of transcriptome and metabolome analyses helps identify candidate genes and regulatory elements for breeding programs (Chen et al., 2025; Lee et al., 2025).

7.4 Reconstructing regulatory networks for flavonoid biosynthesis under environmental adaptation

Multi-omics approaches and network modeling have revealed the complex regulatory networks controlling flavonoid biosynthesis, including responses to environmental factors such as light, temperature, and stress. Understanding these networks enables the reconstruction of regulatory pathways to optimize flavonoid production under diverse environmental conditions, supporting both crop improvement and adaptation (Qin et al., 2020; Misra et al., 2022).

8 Concluding Remarks

Recent multi-omics studies have revealed the complex genetic and biochemical networks underlying flavonoid biosynthesis in tea plants. Structural genes (for instance, PAL, CHS, F3H, DFR, ANS, UGTs) and regulation transcription factors (the MYB, bHLH, and WD40 members, particularly) have been identified as being crucial in flavonoid accumulation and control of composition. Light, shading, and nutritional status regulate these pathways via signal transduction networks (e.g., UVR8-mediated signaling), which affect gene expression as well as metabolite profiles. Protein-protein interactions and post-translational modifications further refine the biosynthetic machinery leading to flavonoid diversity and abundance in different tissues and developmental stages.

Despite significant progress, several challenges remain. The precise mechanisms of environmental signal integration, the functional redundancy among gene family members, and the dynamic regulation of flavonoid transport and storage are not fully understood. Technical bottlenecks include the limited functional validation of candidate genes, difficulties in manipulating complex regulatory networks, and the need for high-resolution spatial and temporal omics data. Additionally, translating molecular insights into practical breeding strategies for improved tea quality and stress resilience remains a major hurdle.

Future research will be complemented by the integration of genomics, transcriptomics, proteomics, and metabolomics to construct integrated regulatory networks and predictive models. Improvements in gene editing, single-cell omics, and high-throughput phenotyping will speed functional validation and targeted breeding. Interdisciplinary approaches adopting plant biology, computational modeling, and synthetic biology hold promise for engineering tea plants with optimal flavonoid profiles, enhanced health benefits, and enhanced tolerance to environmental stresses.

Acknowledgments

The authors sincerely thank Ms. Liu for her generous support and assistance in the process of information collection and data organization. The authors also extend their heartfelt gratitude to the two anonymous peer reviewers for their valuable comments and suggestions during the review process. 

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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