Integrative Transcriptomic and Metabolomic Analyses of Time-of-Day Variation of Quality-Related Metabolites in Fresh Tea Leaves

Abstract

Green tea quality is largely determined by the metabolite profile of fresh leaves. However, the time-of-day-dependent dynamics of these metabolites remain largely unknown in Xinyang Maojian (XYMJ), a premium Chinese green tea. In this study, we performed the first integrative transcriptomic and metabolomic analysis of Camellia sinensis cv. Xinyang 10 shoots (one bud and one leaf) sampled at 7:00, 13:00, and 18:00 under field conditions with light intensities of 19.2, 113, and 5.4 klx, respectively. We identified 525 differentially accumulated metabolites and 19,767 differentially expressed genes exhibiting distinct time-of-day-dependent patterns. Physiological measurements confirmed significant fluctuations in starch, soluble sugars, chlorophyll, relative water content, and polyphenols throughout the daytime. A key finding was a daytime carbon allocation trade-off: primary metabolism (starch biosynthesis, glycolysis, TCA cycle) peaked at 13:00, whereas secondary metabolism (flavonoids, theaflavins, phenolic acids, anthocyanins) dominated at 18:00, supported by strong negative correlations between primary and secondary metabolic modules. Chlorophyll and oligomeric catechins peaked at 7:00; theaflavins at 13:00; and starch, soluble sugars, theanine, and organic acids at 18:00. Light-responsive transcription factors (bZIP, NF-Y, HD-Zip, SPL, ARF, MADS) and other regulators (MYB, AP2/ERF, WRKY, NAC, GRAS, bHLH) exhibited time-specific expression, sequentially modulating flavonoid, caffeine, and theanine biosynthesis, along with specific gene modules including SS3/SS4 (starch synthesis), BAM3 (starch degradation), FBA1 (carbon fixation), CYP72A219 (terpenoid metabolism), and L7A (theaflavin biosynthesis). Evening-harvested leaves accumulated higher levels of theanine (umami) and soluble sugars (sweetness), whereas morning leaves were enriched in astringent catechins and flavonols. This multi-omics dissection of time-of-day-dependent metabolism in XYMJ tea provides a scientific basis for time-of-day harvesting strategies and graded processing of tea products.