Tea quality is shaped by a delicate chemical balance. Catechins largely contribute bitterness and astringency, theanine provides freshness and umami, and caffeine adds characteristic stimulation and taste complexity. Previous studies have clarified many metabolic pathways in tea plants, but most transcriptomic analyses used mixed tissue samples, making it difficult to see where specific genes act inside developing shoots. Single-cell approaches can reveal cell heterogeneity, yet often lose the spatial context that connects gene activity with tissue structure. Based on these challenges, in-depth research is needed to map spatial gene expression and uncover precise regulatory mechanisms of characteristic metabolites in tea shoots.
A research team from the Anxi College of Tea Science, College of Horticulture, Fujian Agriculture and Forestry University, and the Fujian Collaborative Innovation Center for Green Cultivation and Processing of Tea Tree in Universities reported (DOI: 10.1093/hr/uhag003) the study in Horticulture Research on January 6, 2026. Using tea tender shoots from Camellia sinensis var. sinensis cv. ‘Tieguanyin’, the researchers constructed a spatially resolved transcriptomic atlas covering the apical bud, young leaf, and tender stem, and investigated how tissue-specific gene programs regulate tea's characteristic metabolites.
The team applied 10× Visium-based spatial transcriptomics (ST) to intact shoot sections, integrating histological structure with marker-gene annotation. The genome-wide expression landscape was divided into nine spatial coexpression clusters, corresponding to cell and tissue regions such as epidermis, mesophyll, vascular bundles, phloem, xylem, pith, and parenchyma. Pseudotime trajectory analysis further traced developmental transitions in bud and leaf tissues, showing how early unspecialized cells progress toward photosynthetic, vascular, defense-related, and metabolically active states. The researchers then mapped genes involved in catechin, theanine, and caffeine metabolism. Catechin-related genes, including CsANR and CsF3H, were enriched in specific bud and young leaf regions, while theanine hydrolysis genes such as CsGGT2 and CsHO1 showed distinct spatial activity in aerial tissues. By combining spatial coexpression patterns with promoter-binding predictions, the team identified CsTCP4 as a candidate coordinator of catechin and theanine metabolism. Functional assays showed that the CsTCP4 protein localizes to the nucleus, has transcriptional activation activity, and can promote the expression of CsANR, CsF3H, CsGGT2, and CsHO1.
The authors said the study offers a more detailed way to understand tea flavor formation by placing gene activity back into its tissue context. Instead of treating a young shoot as a uniform sample, the spatial map shows where different metabolic decisions are likely being made. They said the discovery of CsTCP4 is especially meaningful because it connects two major taste-related processes: the production of catechins and the breakdown of theanine. This provides a molecular explanation for how tea plants may shift the balance between bitter-astringent and fresh-umami qualities during shoot development.
These findings provide a valuable reference for tea biology, quality improvement, and molecular breeding. By identifying spatially active metabolic genes and a regulatory factor that influences both catechin accumulation and theanine degradation, the study points to potential targets for fine-tuning flavor quality in elite tea cultivars. The spatial transcriptome atlas may also support future studies on how light, nitrogen supply, developmental stage, or environmental stress shape tea chemistry. Beyond tea, the work demonstrates how spatial transcriptomics can help uncover hidden regulatory networks in woody horticultural crops, where tissue complexity often makes conventional gene-expression analysis insufficient.
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References
DOI
10.1093/hr/uhag003
Original Source URL
https://doi.org/10.1093/hr/uhag003
Funding information
This work was supported by grants from the National Natural Science Foundation of China (32502780), the Natural Science Foundation of Fujian Province (2025 J08070), the Young Backbone Faculty Fostering Fund of Anxi Tea College, Fujian Agriculture and Forestry University (ACKY2024002), and the Special Fund for Science and Technology Innovation of Fujian Zhang Tianfu Tea Development Foundation (FJZTF01).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.