1 Introduction

Tea is one of the most popular beverages in the world. Its aroma and flavor quality are the core factors influencing consumers’ preferences and market value (Yao et al., 2024). Aroma substances and flavor metabolites (such as tea polyphenols, amino acids, caffeine and terpene volatiles) not only determine the taste and aroma of tea, but are also closely related to health functions (Zhao et al., 2022; Liu et al., 2025). Different tea tree varieties and growing environments can cause significant differences in aroma and flavor components. High-quality tea often contains some specific aromatic compounds and flavor substances, such as (R) -linallinol. These components can directly enhance the market competitiveness of tea (Li et al., 2022b; Liu et al., 2025).

Traditional breeding methods have achieved certain results in increasing the yield and stress resistance of tea trees, but their effects are limited when it comes to improving complex quality traits such as aroma and flavor. They have long cycles, low efficiency, and it is difficult to precisely target the key genes or metabolic pathways that regulate aroma and flavor (Zhao et al., 2022). The asexual reproduction and complex genetic background of tea plants also make the directional improvement of superior traits more difficult (Zhang et al., 2021; Chen et al., 2023). Therefore, more efficient and precise molecular breeding methods are needed to break through these limitations.

This study analyzed the genetic basis and molecular mechanisms related to aroma and flavor, compared the advantages and challenges of different molecular breeding techniques such as genomic selection, genome-wide association analysis, and mutagenesis breeding in improving quality traits, and proposed the future development direction of molecular breeding for tea tree quality. This research aims to provide theoretical basis and technical reference for the quality improvement of tea trees, promoting the precise improvement and sustainable development of high-quality tea varieties.

2 Biochemical and Genetic Basis of Aroma and Flavor in Tea

2.1 Key volatile and non-volatile compounds contributing to tea aroma and flavor

The aroma and flavor of tea are jointly determined by a variety of volatile and non-volatile compounds. The main volatile components include monoterpenoids, sesquiterpenoids, aldehydes, ketones and heterocyclic compounds, etc. These substances endow tea with various flavors such as floral, fruity and nutty aromas (Yin et al., 2022; Yu et al., 2023; Yang et al., 2024). Non-volatile components, such as catechins, amino acids, sugars and caffeine, can affect the freshness, bitterness and richness of tea soup (Xia et al., 2017; Wang et al., 2022). Different types of tea vary greatly in the types and contents of these components, which determines their respective flavor characteristics (Han et al., 2016; Liu et al., 2023; Ma et al., 2023).

2.2 Biosynthetic pathways for terpenoids, phenylpropanoids, and amino acid derivatives

Terpenoids are mainly synthesized through the mevalonic acid (MVA) and methyl erythritol phosphate (MEP) pathways. Terpene synthase (TPS) is the key enzyme. In high-aroma tea tree varieties, this gene family shows significant amplification (Xia et al., 2017; Wang et al., 2021a). Phenylpropanes are derived from phenylalanine and are generated through multiple reactions such as phenylalanine ammonia-lyase (PAL) (Yin et al., 2022). Amino acid derivatives are derived from the degradation and transformation of amino acids such as tryptophan and phenylalanine (Yang et al., 2024). Fatty acid degradation and carotenoid cleavage can also produce key aroma substances, such as β -violet ketone and β -cyclocitral (Yin et al., 2022).

2.3 Genetic determinants and transcriptional regulation of flavor-related metabolites

The genetic basis of tea tree aroma and flavor is very complex, involving many structural genes and regulatory factors. In high-aroma varieties, the amplification and structural changes of terpene synthase (TPS) family genes promoted the accumulation of terpene aroma substances (Wang et al., 2021a). The synthetic genes of phenylpropanes and amino acid derivatives are also affected by structural variations and allelic imbalance (Xia et al., 2017). Transcription factors such as MYB and bHLH are crucial in regulating the gene expression of flavor metabolism pathways (Gohain et al., 2012). Li et al. (2024) found that epigenetic regulation, such as reduced methylation in the promoter region and enhanced chromatin accessibility, would increase the expression of key aroma synthesis genes, leading to a greater accumulation of specific aroma components. Alternative splicing (AS), as a post-transcriptional regulatory mechanism, also affects the expression of flavor-related genes and the formation of aroma substances (Qiao et al., 2024).

3 Molecular Breeding Tools and Strategies

3.1 Marker-assisted selection (MAS) for aroma and flavor traits

Marker-assisted selection (MAS) can efficiently screen out genotypes related to aroma and flavor through the linkage relationship between molecular markers and target traits. In tea plants, MAS has been used to screen genotypes related to the synthesis of aromatic substances (such as terpenoids, alcohols, and esters), enhancing the breeding efficiency of high-quality aroma and flavor traits. For instance, the contents of certain aromatic substances (such as (R)-linalool, β -violetone, etc.) are closely related to the expression levels of their synthase genes. MAS can help quickly identify highly expressed genotypes for breeding (Li et al., 2022b; Liu et al., 2025). In addition, MAS has also shown great value in screening tea tree germplasms with flavor-related traits such as high amino acids and low caffeine (Zhao et al., 2022).

3.2 Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS)

QTL mapping and GWAS are core methods for studying the genetic basis of tea tree aroma and flavor. Through high-density molecular markers and large-scale population analysis, researchers have identified multiple QTLS and candidate genes related to aroma and flavor in tea plants. GWAS studies based on pan-genome and large-scale SNP data have revealed a strong association between allelic variations and flavor chemical components (such as flavonoids, terpenoids, etc.), providing targets for molecular design breeding (Yu et al., 2020). The combined use of QTL and GWAS helps to precisely locate the major genes and regulatory networks that affect aroma and flavor, and accelerate the breeding of high-quality tea tree varieties (Zhang et al., 2021; Chen et al., 2023).

3.3 Genomic selection (GS) and haplotype-based breeding approaches

Genomic selection (GS) utilizes genome-wide marker information to predict an individual's breeding value and is suitable for improving complex traits controlled by multiple genes, such as aroma and flavor. GS can shorten the breeding cycle and improve the efficiency of seed selection. Recently, with the establishment of high-quality reference genomes and haplotype assembly of tea plants, haplotype breeding strategies have gradually emerged. Haplotype resolution is helpful for analyzing allele-specific expression and its influence on aroma and flavor traits, as well as promoting targeted gene improvement and precision breeding (Zhang et al., 2021; Chen et al., 2023). The development of pan-genome resources also provides more genetic diversity support for GS and haplotype breeding.

4 Role of Functional Genomics and Omics Technologies

4.1 Transcriptomics and metabolomics for candidate gene discovery

Researchers can analyze the relationship between gene expression and metabolite accumulation at different developmental stages, in different tissues or under different treatment conditions through high-throughput transcriptome sequencing (RNA-seq) and metabolite profiling. The combined analysis of the transcriptome and metabolome has discovered many key genes related to the synthesis of flavor substances such as amino acids, flavanols, and caffeine. Candidate genes regulating these metabolic pathways have also been identified through the gene-metabolite network (Wei et al., 2018; Zhang et al., 2018). In specific varieties, haplotype assembly and allele-specific expression analysis are helpful for identifying structural genes such as CsMCT, CsGGPPS2, and CsTPS10 that play key roles in aroma formation (Gu et al., 2023). These results provide valuable genetic resources and molecular markers for molecular breeding.

4.2 Epigenomic regulation of aroma-related genes

Epigenomics (such as DNA methylation and histone modification) is also important in regulating the expression of genes related to the aroma of tea plants. Although there are not many direct studies on the epigenetic regulation of aroma genes in tea plants, existing studies have found through haplotype assembly and allele-specific expression analysis that the expression of key genes in the aroma synthesis pathway varies in different tissues and developmental stages, which may be related to epigenetic regulation (Gu et al., 2023). Population genomics and selection signal analysis also revealed that metabolic pathway genes related to aroma and flavor were subjected to intense selection pressure, suggesting that epigenetic regulation may play an important role in the evolution and domestication of aroma traits in tea plants (Zhang et al., 2021).

4.3 Integration of multi-omics for systems-level understanding

Integrating multi-omics data provides new ideas for understanding the molecular mechanisms of tea tree aroma and flavor at the systematic level. The construction of the pan-genome revealed the structural variations and functional diversity of aroma and flavor-related genes in tea plants, and also provided a scientific basis for genome-wide association analysis and molecular design breeding (Chen et al., 2023; Tariq et al., 2024). Researchers can comprehensively analyze the genetic basis of aroma and flavor traits from gene variation, expression regulation to metabolite accumulation by integrating different omics data (Wei et al., 2018; Zhang et al., 2018). The combined analysis of the pan-genome and multi-omics revealed the functional differentiation of the core genome and the variable genome, providing theoretical support and technical tools for precise molecular breeding of aroma and flavor traits (Tariq et al., 2024).

5 Genome Editing and Synthetic Biology Applications

5.1 CRISPR/Cas-based gene editing for trait improvement

CRISPR/Cas9 is an efficient gene editing tool. The research identified 248 million potential editing sites in tea plants, covering all gene structural elements. Many of these sites are concentrated in regions related to secondary metabolites and amino acid biosynthesis, providing a basis for the precise regulation of aroma and flavor traits. Theoretically, by targeting and regulating the genes of key metabolic pathways, the aroma and flavor of tea can be improved in a targeted manner. However, due to the fact that the highly hybrid and transformation system of tea plants is still not perfect, there are still technical difficulties in practical application. However, the discovery of these gene editing sites has provided important resources for subsequent molecular breeding (Figure 1) (Li et al., 2023).

Figure 1 Distribution and analysis of editing sites and multi-elements in Camellia sinensis (Adopted from Li et al., 2023) Image caption: (A) Chromosome of the Camellia sinensis genome. (B-F) Density heatmap of the different element. (B) GC content; (C) Gene density; (D) GQ density; (E) SSR density; (F) PAM density; (G) Standardised fold plot of correlation of various elements in the 120~130 Mbp interval of chromosome 5 (Adopted from Li et al., 2023)

5.2 Promoter engineering for aroma biosynthetic pathway enhancement

The expression of key genes in aroma-related metabolic pathways is regulated by promoters. Promoter engineering can enable target genes to be expressed more efficiently in specific tissues or developmental stages, enhancing the synthesis of aroma substances. The specific expression of terpene synthesization-related genes (such as the CsTPS family) and their alleles in tea plants is closely related to the formation of aroma. The optimization of promoter regulation is expected to achieve the directional accumulation of aroma components (Gu et al., 2023). Genome-wide and haplotype assembly studies have revealed the selected key genes in the aroma biosynthesis pathway, providing valuable targets for promoter engineering (Zhang et al., 2021).

5.3 Synthetic biology approaches for metabolic pathway optimization

Synthetic biology can efficiently synthesize aroma and flavor substances by modularly reconstructing and optimizing metabolic pathways. There is multi-copy amplification and expression regulation of genes related to aroma and flavor substances (such as catechins, theanine, and caffeine) in tea plants, laying the foundation for the application of synthetic biology (Wang et al., 2021b). By integrating multi-gene expression, metabolic flow redirection and regulatory element optimization, it is expected to increase the yield and variety of target metabolites. Synthetic biology can also utilize heterologous expression systems to analyze and reconstruct the functions of aroma-related enzymes in tea plants, providing theoretical and technical support for molecular breeding (Zhou et al., 2017).

6 Environmental and Agronomic Interactions

6.1 Effects of terroir factors (altitude, soil, climate) on flavor profiles

Terroir factors, such as altitude, soil type and climatic conditions, have a significant impact on the accumulation of flavor substances in tea trees. Different geographical environments can cause significant differences in the content of secondary metabolites (such as catechins, amino acids, and terpenoids) in tea, which in turn determine the aroma and flavor characteristics of tea. For instance, some tea tree groups can accumulate more polyphenols and aromatic substances in high-altitude areas. Low temperature and light changes can also regulate the expression of flavor-related genes (Yu et al., 2020; Zhao et al., 2022). In addition, supplementing trace elements (such as selenium) in the soil can enhance the freshness and aroma of tea by regulating amino acid and flavonoid metabolic pathways (Zhang et al., 2025). The interaction between these terroir factors and genetic background is an environmental variable that needs to be given key consideration in molecular breeding.

6.2 Epigenetic and transcriptional responses to environmental cues

Tea plants have complex epigenetic and transcriptional regulatory mechanisms when exposed to environmental stress. Studies have found that environmental changes can induce differential expression of flavor-related genes, such as terpene synthases and amino acid synthases, thereby affecting the accumulation of aromatic substances (Yu et al., 2020; Zhao et al., 2022; Wu et al., 2023). Post-harvest stress can regulate the expression of genes in the aromatic synthesis pathway through transcription factors (such as CsMYC2c), resulting in differences in aroma components among different varieties (Wu et al., 2023). Treatment with exogenous elements (such as selenium) can also significantly change the expression profile of flavor metabolism genes and improve the quality of tea (Zhang et al., 2025). These molecular responses provide potential targets for molecular breeding and are helpful in screening out superior genotypes with strong environmental adaptability and stable flavor.

6.3 Breeding for stable flavor traits across environments

Pan-genome and population genome studies have shown that flavor traits are regulated by multiple genes and have abundant allelic variations and selection signals (Zhang et al., 2021). Through genome-wide association analysis (GWAS) and molecular marker-assisted selection, the major flavor genes and their environmental interaction effects can be precisely located (Rohilla et al., 2022; Chen et al., 2023). Combining epigenetic and transcriptomic data, along with multi-environmental phenotypic assessment, is helpful for screening flavor genotypes that perform well under various terroir conditions and achieving genetic stability of flavor traits (Yu et al., 2020; Zhang et al., 2021; Zhao et al., 2022). Novel mutagenesis breeding (such as aerial mutagenesis) also provides new approaches for enhancing flavor diversity and environmental adaptability (Ye et al., 2024a).

7 Case Study: Molecular Breeding for Aroma Improvement in Tea

7.1 Selection of high-aroma tea cultivars for genomic analysis

The screening of high-aroma tea tree varieties usually relies on rich germplasm resources and phenotypic assessment. Researchers used genome-wide association study (GWAS) and pan-genome construction to sequence the genomes of 22 representative superior varieties, revealing the genetic diversity and functional variations that affect aroma and flavor. These achievements provide important genetic resources for molecular breeding (Zhang et al., 2021; Chen et al., 2023). Metabolomics analysis systematically identified the aroma and flavor metabolites of 136 tea plant samples, clarifying the accumulation patterns of characteristic metabolites among different strains (Yu et al., 2020).

7.2 Identification of key alleles and markers for flavor biosynthesis

Researchers have identified key genes and their allelic variations related to aroma and flavor by using genomic and transcriptomic data. The high expression of the linalool synthase gene is closely related to the accumulation of (R)-linalool in high-aroma varieties and is an important molecular indicator of the aroma quality of dark tea (Figure 2) (Li et al., 2022b; Liu et al., 2025). Key enzymes in the aromatic amino acid metabolic pathway (such as AAATs) and their allele variations have also been confirmed to affect the formation of aromatic compounds (Wang et al., 2019). Molecular markers (such as SNP, SSR) have been developed to assist in the selection of high-aroma and high-flavor varieties and accelerate the breeding process.

Figure 2 Chiral linalool contents in Yinghong No. 9 in different seasons and tissues (Adopted from Liu et al., 2025) Image caption: (A) (R)-Linalool and (S)-linalool contents in YJBT in different seasons. D.W., dry weight. (B) (R)-Linalool and (S)-linalool contents in Yinghong No. 9 fresh leaves in different seasons. F.W., fresh weight. (C) Schematic diagram of different Yinghong No. 9 tissues. (D) (R)-Linalool and (S)-linalool contents in different grades of YJBT; JYH, Jinyinghong; JMH, Jinmaohao; JH, Jinhao. (E) (R)-Linalool and (S)-linalool contents in different Yinghong No. 9 fresh leaf tissues collected in March 2024. Data are presented as the mean ± SD of three replicates. * , p ≤ 0.05; * *, p ≤ 0.01 (Adopted from Liu et al., 2025)

7.3 Field validation and sensory evaluation of improved lines

The improved lines obtained through molecular breeding need to be tested at multiple points in the field and comprehensively verified by combining metabolite analysis and sensory evaluation. Field experiments have shown that new breeding methods such as aerial mutagenesis can significantly increase the content of volatile aroma substances in tea and enhance sensory characteristics such as fruity aroma and floral aroma (Ye et al., 2024a; Ye et al., 2024b). Sensory evaluation combined with gas chromatography-olfactory analysis (GC-O) and flavor dilution analysis (FD) can quantitatively identify key aroma active substances and be correlated with molecular labeling results to ensure the stable performance of improved strains in actual production (Yang et al., 2021; Li et al., 2022a).

8 Challenges and Future Prospects

8.1 Technical challenges in linking genotype to phenotype for complex traits

The aroma and flavor of tea plants are complex traits controlled by multiple genes and are also strongly influenced by the environment. This makes the precise association between genotype and phenotype very difficult. Although pan-genome and large-scale population genomics studies have identified the key alleles that affect flavor and revealed their relationships with chemical components, the genetic basis of complex traits has not yet been fully clarified. In particular, the effects of polygenic interaction, epigenetic regulation and environmental factors are still difficult to be comprehensively analyzed (Yu et al., 2020; Li et al., 2022b; Chen et al., 2023). In addition, tea plants have long adopted asexual reproduction, and their genomes are complex and have a high degree of heterozygosis, which also makes the development of molecular markers and the localization of functional genes more challenging (Zhang et al., 2021; Chen et al., 2023).

8.2 Integration of AI, big data, and precision breeding tools

With the continuous accumulation of high-throughput omics, phenomics and environmental data, artificial intelligence (AI) and big data analysis have provided new opportunities for the genetic analysis and molecular design breeding of complex traits. AI can integrate multi-omics data for complex trait prediction and candidate gene screening, improving the efficiency of molecular marker-assisted selection and gene editing (Yu et al., 2020). Nowadays, precision breeding tools (such as CRISPR/Cas gene editing and pan-genome association analysis) have begun to be used for the improvement of aroma and flavor traits of tea plants, but their application in multi-gene complex traits still requires further optimization and verification (Zhang et al., 2021; Chen et al., 2023).

8.3 Prospects for climate-resilient, high-quality tea breeding programs

Climate change will affect the quality and yield of tea trees. Future breeding needs to take into account aroma, flavor and stress resistance. Population genomics studies have found that tea plants have developed adaptive genes to environmental factors such as cold stress during domestication, suggesting that molecular breeding has the potential to achieve simultaneous improvement of high quality and climate adaptability (Zhang et al., 2021; Chen et al., 2023). Through the exploration of specific germplasm resources and functional genes, it is expected to cultivate new varieties that have both excellent flavors and can adapt to environmental changes, promoting the sustainable development of the tea industry (Yu et al., 2020; Li et al., 2022b; Zhao et al., 2022).

Acknowledgments

The authors appreciate the comments from two anonymous peer reviewers on the manuscript of this study.

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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