Transcriptomic and biochemical analyses revealed the dynamic regulatory mechanisms underlying leaf morphogenesis in Camellia sinensis

Tea leaf development is a biological process marked by sequential morphogenesis that directly affects tea yield and quality. Despite their importance, the dynamic regulatory mechanisms governing these developmental stages remain poorly understood. In this study, we utilized tea buds, first leaves, second leaves, and third leaves from tea plants as experimental materials. By integrating transcriptomic sequencing with biochemical analysis, we systematically elucidated the transcriptional-metabolic co-regulatory network underlying leaf morphogenesis. The findings revealed significant differences in the leaf transcriptomes across developmental stages, with the most pronounced differentiation observed between buds and mature leaves. The comparison of bud vs. 3 rd leaf identified the highest number (6, 854) of differentially expressed genes, which were primarily concentrated in the KEGG metabolic pathways. Core metabolites, such as catechins, free amino acids, and alkaloids, were predominantly enriched in buds and young leaves, with most exhibiting a significant decline as the leaves matured. However, O -methylated catechins were significantly enriched in mature leaves. The expression of these core metabolites is regulated by differentially expressed genes in the phenylpropanoid and flavonoid pathways ( CHS , ANS , SCPL , OMTs , etc.), theanine biosynthesis genes ( ALaDC , ALaAT , TS , etc.), and purine alkaloid biosynthesis genes ( IMPDH , SAMS , TCS , etc.). Correlation analysis indicated that most free amino acids (L-The, Glu, Gln, Asp, Ala, and GABA) exhibited significant positive correlations with alkaloids and catechins (C, GC, CG, EC, and ECG), whereas correlations with O -methylated catechin components were weak. Real-time quantitative PCR analysis revealed that 108 genes were significantly differentially expressed, with functions primarily involving cell wall synthesis and remodeling ( CER3 , PRP4 , EXPA1 , etc.), photosynthesis ( ndhL ), plant hormone signaling regulation ( SAUR23 , CYP85A1 , IAA14 , etc.), cell cycle ( CYCD1-1 , CYCA2-4 ), signal transduction ( MKK6 , MLO6 ), defense and secondary metabolism ( STR1 ), and transcription factors (GRF1, MYB17, bHLH94, etc.). Furthermore, the promoter regions of functional genes related to leaf development showed significant enrichment of MYB and MYC transcription factors, as well as cis-regulatory elements for hormones (ABRE, ERE, TCA-element), light (GT1-motif, GATA-motif, TCT-motif), and stress signals (ARE, STRE, W box). This study identified the core genes and metabolic mechanisms underlying leaf morphogenesis in tea plants, providing a theoretical basis for high-quality cultivation of tea.