Tea leaves contain abundant flavonoids, amino acids, and phytohormones that shape flavor, aroma, and nutritional value. Although individual metabolic pathways and regulatory genes have been characterized, how leaf development and metabolite synthesis are integrated remains poorly understood. The bud-to-leaf transition involves coordinated cell proliferation, differentiation, and metabolic reprogramming. However, most previous studies relied on bulk tissue analyses, masking cell-type-specific regulation. In addition, interactions among microRNAs, transcription factors, and hormone pathways during this transition have not been systematically resolved. Due to these limitations, there is an urgent need for in-depth, cell-resolution investigations into the coordinated regulation of leaf development and metabolism in tea plants.
In a study published (DOI: 10.1093/hr/uhaf281) on January 1, 2026, in Horticulture Research, scientists from the Tea Research Institute of the Chinese Academy of Agricultural Sciences and collaborating institutions applied single-nucleus RNA sequencing to tea buds and successive leaves. By integrating transcriptomic and metabolomic profiling, the team constructed a high-resolution atlas of eight major cell types and 17 cell clusters. Their analyses identified developmental-stage-specific hormone patterns and revealed that genes such as CsmiRNA396b, CsUGT94P1, CsTCP3, and CsTCP14 play central roles in coordinating leaf growth and flavonoid biosynthesis.
The researchers profiled nuclei from buds and the first three leaves, identifying eight major cell types, including palisade mesophyll and proliferating cells. As leaves matured, the proportion of palisade mesophyll cells increased, while proliferating cells decreased. Pseudo-time trajectory analysis revealed branching developmental paths accompanied by activation of genes associated with chloroplast biogenesis and phenylpropanoid metabolism.
Metabolomic profiling uncovered stage-specific hormonal shifts. Auxin, cytokinin, abscisic acid, and jasmonic acid levels declined during maturation, whereas GA8 increased. In contrast, flavonoids—particularly flavonol glycosides and catechins—accumulated progressively, while amino acids such as L-theanine were most abundant in buds and declined in later stages.
Spatial transcriptomic analysis showed that flavonoid biosynthetic genes were predominantly expressed in palisade mesophyll cells. Enzyme assays confirmed that CsUGT94P1 catalyzes the glycosylation of flavonols, explaining the increase in flavonoid glycosides during development. Meanwhile, CsmiRNA396b regulated leaf size by repressing CsGRF1, CsGRF2, and CsGRF3. Two transcription factors encoded by CsTCP3 and CsTCP14 acted antagonistically: CsTCP3 promoted flavonoid accumulation but restricted leaf expansion, whereas CsTCP14 enhanced leaf growth while suppressing flavonoid biosynthesis.
“Our study shows that bud-to-leaf development represents coordinated cellular and metabolic reprogramming rather than simple growth,” the authors explain. “By linking cell-type-specific gene expression to metabolite dynamics, we demonstrate how regulatory networks involving CsmiRNA396b, CsTCP3, CsTCP14, and CsUGT94P1 integrate developmental control with flavor-related metabolism.” The researchers note that resolving these mechanisms at single-cell resolution provides a molecular foundation for improving both tea yield and quality.
The findings offer practical implications for tea breeding and quality optimization. By identifying genes such as CsUGT94P1 and CsTCP3 that influence flavonoid glycoside accumulation, breeders may be able to modulate bitterness and astringency without compromising leaf growth. The discovery that CsmiRNA396b regulates leaf size also opens avenues for improving shoot architecture and harvest efficiency. Beyond tea, the study establishes a framework for dissecting developmental–metabolic coordination in other perennial crops. As single-cell technologies continue to advance, integrated multi-omics strategies are expected to transform our understanding of crop quality formation at cellular resolution.
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References
DOI
10.1093/hr/uhaf281
Original Source URL
https://doi.org/10.1093/hr/uhaf281
Funding information
This work was supported by Central Public-interest Scientific Institution Basal Research Fund (No. 1610212024002), the China Agricultural Research System of MOF and MARA (CARS-019), and the Chinese Academy of Agricultural Sciences through the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2021-TRICAAS), Zhejiang Provincial Natural Science Foundation of China, under Grant No. LZ22C160008, and Jiangxi Province Talent Plan (jxsq2023102020) to L.C.
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.