Metabolomics and Transcriptomics Analyses Reveal Nitrogen Influences on the Accumulation of Flavonoids and Amino Acids in Young Shoots of Tea Plant ( Camellia sinensis L.) Associated with Tea Flavor

Integrative transcriptomic-physiological analysis deciphers nitrogen-mediated carbon reallocation balancing growth and flavonoid metabolism in Epimedium pubescens

Nitrogen availability critically shapes medicinal plant quality by coordinating the "growth-secondary metabolism" trade-off, yet its regulatory mechanisms remain elusive in the non-model species Epimedium pubescens. Through physiological-transcriptomic integration under five nitrogen levels (0, 3.5, 7.5,15, 22.5 mM NO3 -), we demonstrated that moderate nitrogen (MN: 7.5 mM NO3 -) optimally balanced biomass accumulation (22%-53% higher than low nitrogen [LN: 0 mM NO3 -] and high nitrogen [HN: 22.5 mM NO3 -]) with maximal Icariin-type flavonoid production (19%-34% higher than LN/HN). Extreme nitrogen stresses (LN/HN) impaired photosynthetic efficiency (18%-20% reduction), disrupted carbon-nitrogen homeostasis, and restricted flavonoid biosynthesis by hindering carbon reallocation (soluble sugars reduced by 26%-27%, starch by 30%-43%). Time-series transcriptomics revealed distinct response dynamics: LN triggered active transcriptional reprogramming at mid-stage (36 days after treatment, DAT), whereas HN responses were delayed to late-stage (48 DAT). Weighted gene co-expression network analysis (WGCNA) identified the grey60 module as a hub coordinating carbon-nitrogen metabolism and mRNA processing. A tripartite regulatory network linking nitrogen-responsive genes (e.g., EpF3H, UGT), Icariin-type flavonoid/carbon metabolism (e.g., icariin, soluble sugars), and growth phenotypes (e.g., biomass, photosynthesis) elucidated how nitrogen optimizes the trade-off between medicinal quality and yield in E. pubescens. This study provides molecular targets for precision nitrogen management to enhance both medicinal quality and yield, while establishing an integrative framework combining physiological and transcriptomic analyses to investigate metabolic trade-offs in non-model plants.

A Comprehensive Understanding of Camellia sinensis Tea Metabolome: From Tea Plants to Processed Teas

Tea (Camellia sinensis) is one of the most popular nonalcoholic beverages in the world, second only to water. Six main types of teas are produced globally: green, white, black, oolong, yellow, and Pu-erh. Each type has a distinctive taste, quality, and cultural significance. The health-promoting effects of tea are attributed to the complex metabolite compositions present in tea leaves. These metabolite compositions vary in response to different factors. In addition to manufacturing processes in processed tea, the primary factors influencing variations of fresh tea leaf metabolites include genetics, cultivation management, and environmental conditions. Metabolomics approaches, coupled with high-throughput statistical analysis, offer promising tools for the comprehensive identification and characterization of tea leaf metabolites according to growing conditions, cultivation practices, manufacturing processes, seasonality, climate, cultivars, and geography. This review highlights the distinctive variations in fresh tea leaf metabolites, which change in response to various factors, using a metabolomics approach, which are also extended to various processed teas.

Combined analysis of proteomics and metabolism reveals critical roles of oxidoreductase activity in mushrooms stimulated by wolfberry and sea buckthorn substrates

Background

Cultivating edible fungi, particularly Lentinula edodes, efficiently transforms agroforestry byproducts into valuable products. However, the mechanism of the promotive effects of those substrates was largely unknown. This study used wolfberry (WB) and sea buckthorn (SBK) substrates to investigate mushroom fruiting bodies' physiological, proteomics, and metabolism profiling.

Results

Results show that compared to apple wood (AW), the crude protein and fatty acids were substantially enhanced by both WB and SBK treatment. We identified 1409 and 1190 upregulated and downregulated differentially abundant proteins (DAPs) for the SBK versus AW group and observed 929 overlapped DAPs with upregulation patterns. Of these DAPs, carbohydrates and oxidoreductase activity pathways were significantly enriched. Moreover, the enhanced expression of nine genes by WB and SBK was confirmed by qPCR. Metabolism suggests that 66 differentially abundant metabolites overlapped in the list of two comparison groups (WB versus AW and SBK versus AW).

Conclusion

Collectively, we summarized that both WB and SBK stimulate glucose degradation, enhance the expression of gene-related oxidoreductase activity, and promote protein biosynthesis by coordinating with amino acid metabolism. This study highlights the importance of oxidoreductase activity in promoting nutritional value in mushroom fruiting bodies induced by WB and SBK substrates.

L-Theanine Metabolism in Tea Plants: Biological Functions and Stress Tolerance Mechanisms

L-theanine, a unique non-protein amino acid predominantly found in tea plants (Camellia sinensis), plays a pivotal role in plant responses to abiotic stress and significantly influences tea quality. In this review, the metabolism and transport mechanisms of L-theanine are comprehensively discussed, highlighting its spatial distribution in tea plants, where it is most abundant in young leaves and less so in roots, stems, and older leaves. The biosynthesis of L-theanine occurs through the enzymatic conversion of glutamate and ethylamine, catalyzed by theanine synthase, primarily in the roots, from where it is transported to aerial parts of the plant for further catabolism. Environmental factors such as temperature, light, drought, elevated CO2, nutrient unavailability, and heavy metals significantly affect theanine biosynthesis and hydrolysis, with plant hormones and transcription factors playing crucial regulatory roles. Furthermore, it has been demonstrated that applying L-theanine exogenously improves other crops' resistance to a range of abiotic stresses, suggesting its potential utility in improving crop resilience amid climate change. This review aims to elucidate the physiological mechanisms and biological functions of L-theanine metabolism under stress conditions, providing a theoretical foundation for enhancing tea quality and stress resistance in tea cultivation.

Effects of microbial biocontrol agents on tea plantation microecology and tea plant metabolism: a review

The quality of fresh tea leaves is crucial to the final product, and maintaining microbial stability in tea plantations is essential for optimal plant growth. Unique microbial communities play a critical role in shaping tea flavor and enhancing plant resilience against biotic stressors. Tea production is frequently challenged by pests and diseases, which can compromise both yield and quality. While biotic stress generally has detrimental effects on plants, it also activates defense metabolic pathways, leading to shifts in microbial communities. Microbial biocontrol agents (MBCAs), including entomopathogenic and antagonistic microorganisms, present a promising alternative to synthetic pesticides for mitigating these stresses. In addition to controlling pests and diseases, MBCAs can influence the composition of tea plant microbial communities, potentially enhancing plant health and resilience. However, despite significant advances in laboratory research, the field-level impacts of MBCAs on tea plant microecology remain insufficiently explored. This review provides insights into the interactions among tea plants, insects, and microorganisms, offering strategies to improve pest and disease management in tea plantations.

A novel transcription factor CsSNACA2 plays a pivotal role within nitrogen assimilation in tea plants

Tea (Camellia sinensis) is a globally renowned economic crop, with organs such as leaves and buds utilized for consumption. As a perennial foliage crop, tea plants have high-nitrogen consumption and demand but exhibit relatively low nitrogen use efficiency. Exploring the genetic factors involved in nitrogen assimilation in tea plants could lead to improvements in both tea yield and quality. Here, we first conducted transcriptome sequencing on two tissues (roots and young leaves) under two different nitrate levels (0.2 and 2.5 mm KNO3) and at six time points (0, 15, and 45 min; 2 and 6 h and 2 days). Differential gene expression patterns were observed for several genes that exhibited altered expression at 2 h. Clustering and enrichment analyses, along with co-expression network construction, provided evidence for the crucial involvement of CsSNACA2 in nitrogen assimilation. CsSNACA2 overexpression elicited pronounced phenotypic changes in nitrogen-deficient plants. Furthermore, CsSNACA2 suppressed the expression of CsNR (encoding nitrate reductase) and CsCLCa (encoding aNO 3 - /H+ exchanger). Moreover, CsSNACA2 served as a downstream target of CsSPL6.1. In addition, we characterized Csi-miR156e and Csi-miR156k, which directly cleave CsSPL6.1. This study identified a transcription factor module participating in nitrogen assimilation in tea plants, providing a genetic foundation for future innovations in tea cultivar improvement. These results broaden our understanding of the genetic mechanisms governing nitrogen assimilation in dicotyledonous plants.

A glutamine synthetase-Dof transcription factor module regulates nitrogen remobilization from source to sink tissues in tea plants

Nitrogen (N) remobilization from mature leaves to new shoots (NSs) is closely related to the quality of green tea in the spring season, which subsequently determines its economic value. However, the underlying N remobilization mechanism remains poorly understood. Here, we demonstrate that >80% of the recovered 15N was partitioned in the first mature leaves that supply NSs. N-remobilization efficiency (NRE) from mature leaves to NSs varied significantly among tea cultivars. N-fertilization level and NRE showed a significantly positive correlation. Based on weighted gene co-expression network analysis, glutamate metabolism-related genes, including glutamine synthetase genes, CsGSs, were dissected from the interaction network of hub genes regulating N remobilization. Gene expression patterns and the localization of CsGS1.1 in the cytosol and vascular tissue suggest its potential role in N remobilization. Consistent with these findings, source-to-sink N remobilization at the reproductive stage was enhanced in transgenic CsGS1.1-overexpressing plants. Furthermore, we demonstrated that the Dof transcription factor CsDof16 directly binds to the -526 to -426 region of the CsGS1.1 promoter, thereby activating its transcription and regulating N remobilization. Taken together, our findings suggest that the CsDof16-CsGS1.1 module regulates the remobilization of N in the form of glutamate/glutamine from mature leaves to NSs, constituting an important control point in the regulation of source-to-sink N partitioning in tea plants. Our findings can be employed to reduce fertilizer application and promote the development of sustainable tea production.

In Vitro vs. In Vivo Transcriptomic Approach Revealed Core Pathways of Nitrogen Deficiency Response in Tea Plant (Camellia sinensis (L.) Kuntze)

For the first time, we used an in vitro vs. in vivo experimental design to reveal core pathways under nitrogen deficiency (ND) in an evergreen tree crop. These pathways were related to lignin biosynthesis, cell redox homeostasis, the defense response to fungus, the response to Karrikin, amino acid transmembrane transport, the extracellular region, the cellular protein catabolic process, and aspartic-type endopeptidase activity. In addition, the mitogen-activated protein kinase pathway and ATP synthase (ATP)-binding cassette transporters were significantly upregulated under nitrogen deficiency in vitro and in vivo. Most of the MAPK downstream genes were related to calcium signaling (818 genes) rather than hormone signaling (157 genes). Moreover, the hormone signaling pathway predominantly contained auxin- and abscisic acid-related genes, indicating the crucial role of these hormones in ND response. Overall, 45 transcription factors were upregulated in both experiments, 5 WRKYs, 3 NACs, 2 MYBs, 2 ERFs, HD-Zip, RLP12, bHLH25, RADIALIS-like, and others, suggesting their ND regulation is independent from the presence of a root system. Gene network reconstruction displayed that these transcription factors participate in response to fungus/chitin, suggesting that nitrogen response and pathogen response have common regulation. The upregulation of lignin biosynthesis genes, cytochrome genes, and strigalactone response genes was much more pronounced under in vitro ND as compared to in vivo ND. Several cell wall-related genes were closely associated with cytochromes, indicating their important role in flavanols biosynthesis in tea plant. These results clarify the signaling mechanisms and regulation of the response to nitrogen deficiency in evergreen tree crops.

Accumulation characteristics of plant flavonoids and effects of cultivation measures on their biosynthesis: A review

Flavonoids, a kind of secondary metabolites with both edible, medicinal and antioxidant purposes, could be widely used in food, drug processing, forest products, chemical industry and many other fields. Flavonoid production in plant organs were influenced by numerous internal and external factors at various stages, leading to differential gene expression and transcription factors activity. This study reviews the characteristics of major flavonoids categories, their distribution and accumulation in different plant parts and analyzing their molecular mechanisms. The results showed that: (1) Flavonoids exhibited wide distribution in all parts of the plants, with higher concentrations found in shoots system compared to roots sytem, across most species (predominantly accumulated in leaves and flowers). Plant sex, specific growth and development stages are both impacting indicators; (2) Cultivation methods and abiotic stress could affect plants flavonoid biosynthesis, while inappropriate physical treatments and cultivation methods induced stress in plants, prompting the activation of antioxidant mechanisms for flavonoid synthesis as a defence strategy via indirect pathways; (3) Various key genes and transcription factors collaboratively influenced key enzymes activities and regulate flavonoid biosynthesis, forming a complex regulatory network among these genes and transcription factors; (4) Further studies are required to elucidate whether flavonoid synthesis under various cultivation measures follows direct or indirect pathways. Furthermore, exploring methods for flavonoid biosynthesis and accumulation in specific organs or tissues, as well as identifying plant tissues and microorganisms with high efficiency in flavonoid biosynthesis, is essential for achieving targeted cultivation of plants and quantitative flavonoid production.

Integrated transcriptome and metabolism unravel critical roles of carbon metabolism and oxidoreductase in mushroom with Korshinsk peashrub substrates

Edible fungi cultivation serves as an efficient biological approach to transforming agroforestry byproducts, particularly Korshinsk peashrub (KP) branches into valuable mushroom (Lentinus edodes) products. Despite the widespread use of KP, the molecular mechanisms underlying its regulation of mushroom development remain largely unknown. In this study, we conducted a combined analysis of transcriptome and metabolism of mushroom fruiting bodies cultivated on KP substrates compared to those on apple wood sawdust (AWS) substrate. Our aim was to identify key metabolic pathways and genes that respond to the effects of KP substrates on mushrooms. The results revealed that KP induced at least a 1.5-fold increase in protein and fat content relative to AWS, with 15% increase in polysaccharide and total sugar content in mushroom fruiting bodies. There are 1196 differentially expressed genes (DEGs) between mushrooms treated with KP relative to AWS. Bioinformatic analysis show significant enrichments in amino acid metabolic process, oxidase activity, malic enzyme activity and carbon metabolism among the 698 up-regulated DEGs induced by KP against AWS. Additionally, pathways associated with organic acid transport and methane metabolism were significantly enriched among the 498 down-regulated DEGs. Metabolomic analysis identified 439 differentially abundant metabolites (DAMs) in mushrooms treated with KP compared to AWS. Consistent with the transcriptome data, KEGG analysis on metabolomic dataset suggested significant enrichments in carbon metabolism, alanine, aspartate and glutamate metabolism among the up-regulated DAMs by KP. In particular, some DAMs were enhanced by 1.5-fold, including D-glutamine, L-glutamate, glucose and pyruvate in mushroom samples treated with KP relative to AWS. Targeted metabolomic analysis confirmed the contents of DAMs related to glutamate metabolism and energy metabolism. In conclusion, our findings suggest that reprogrammed carbon metabolism and oxidoreductase pathways act critical roles in the enhanced response of mushroom to KP substrates.

In-depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis

Tea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health-related compounds. In this study, we present the construction and analysis of a tea pangenome comprising a total of 11 genomes, with a focus on three newly sequenced genomes comprising the purple-leaved assamica cultivar "Zijuan", the temperature-sensitive sinensis cultivar "Anjibaicha" and the wild accession "L618" whose assemblies exhibited excellent quality scores as they profited from latest sequencing technologies. Our analysis incorporates a detailed investigation of transposon complement across the tea pangenome, revealing shared patterns of transposon distribution among the studied genomes and improved transposon resolution with long read technologies, as shown by long terminal repeat (LTR) Assembly Index analysis. Furthermore, our study encompasses a gene-centric exploration of the pangenome, exploring the genomic landscape of the catechin pathway with our study, providing insights on copy number alterations and gene-centric variants, especially for Anthocyanidin synthases. We constructed a gene-centric pangenome by structurally and functionally annotating all available genomes using an identical pipeline, which both increased gene completeness and allowed for a high functional annotation rate. This improved and consistently annotated gene set will allow for a better comparison between tea genomes. We used this improved pangenome to capture the core and dispensable gene repertoire, elucidating the functional diversity present within the tea species. This pangenome resource might serve as a valuable resource for understanding the fundamental genetic basis of traits such as flavour, stress tolerance, and disease resistance, with implications for tea breeding programmes.

Associations between SNPs and vegetation indices: unraveling molecular insights for enhanced cultivation of tea plant (Camellia sinensis (L.) O. Kuntze)

Background

Breeding programs for nutrient-efficient tea plant varieties could be advanced by the combination of genotyping and phenotyping technologies. This study was aimed to search functional SNPs in key genes related to the nitrogen-assimilation in the collection of tea plant Camellia sinensis (L.) Kuntze. In addition, the objective of this study was to reveal efficient vegetation indices for phenotyping of nitrogen deficiency response in tea collection.

Methods

The study was conducted on the tea plant collection of Camellia sinensis (L.) Kuntze of Western Caucasus grown without nitrogen fertilizers. Phenotypic data was collected by measuring the spectral reflectance of leaves in the 350-1100 nm range calculated as vegetation indices by the portable hyperspectral spectrometer Ci710s. Single nucleotide polymorphisms were identified in 30 key genes related to nitrogen assimilation and tea quality. For this, pooled amplicon sequencing, SNPs annotation and effect prediction with SnpEFF tool were used. Further, a linear regression model was applied to reveal associations between the functional SNPs and the efficient vegetation indices.

Results

PCA and regression analysis revealed significant vegetation indices with high R2 values (more than 0.5) and the most reliable indices to select ND-tolerant genotypes were established: ZMI, CNDVI, RENDVI, VREI1, GM2, GM1, PRI, and Ctr2, VREI3, VREI2. The largest SNPs frequency was observed in several genes, namely F3'5'Hb, UFGTa, UFGTb, 4Cl, and AMT1.2. SNPs in NRT2.4, PIP, AlaDC, DFRa, and GS1.2 were inherent in ND-susceptible genotypes. Additionally, SNPs in AlaAT1, MYB4, and WRKY57, were led to alterations in protein structure and were observed in ND-susceptible tea genotypes. Associations were revealed between flavanol reflectance index (FRI) and SNPs in ASNb and PIP, that change the amino acids. In addition, two SNPs in 4Cl were associated with water band index (WBI).

Conclusions

The results will be useful to identify tolerant and susceptible tea genotypes under nitrogen deficiency. Revealed missense SNPs and associations with vegetation indices improve our understanding of nitrogen effect on tea quality. The findings in our study would provide new insights into the genetic basis of tea quality variation under the N-deficiency and facilitate the identification of elite genes to enhance tea quality.

Comprehensive Analysis of the Yield and Leaf Quality of Fresh Tea (Camellia sinensis cv. Jin Xuan) under Different Nitrogen Fertilization Levels

Reasonable application of nitrogen fertilizer can improve the yield and quality of tea. This study used Jin Xuan as the tested variety and applied nitrogen fertilizer at rates of 0 kg/ha (N0), 150 kg/ha (N150), 300 kg/ha (N300), and 450 kg/ha (N450) in the summer and autumn seasons to analyze the effects of nitrogen application on the quality components and gene expression of tea leaves. The results showed that the N150 treatment significantly increased total polyphenols (TP), total catechins (TC), and caffeine contents, with the most significant increase observed in the content of six monomers of catechins (EGCG, ECG, EGC, GCG, GC, and EC) in the summer. The N300 treatment significantly increased TP and AA contents in the autumn while decreasing TC content. Additionally, the N300 treatment significantly increased caffeine and theanine contents in the autumn. Notably, the N300 treatment significantly increased both summer and autumn tea yields. Multivariate statistical analysis showed that TPs, AAs, TCs, EGC, and caffeine were key factors affecting the quality of Jin Xuan. Furthermore, the N150 treatment upregulated the expression of the phenylalanine ammonia-lyase (PAL) gene, which may increase the accumulation of catechins. In conclusion, it is recommended to apply 150 kg/ha of nitrogen fertilizer in the summer and 300 kg/ha of nitrogen fertilizer in the autumn. This recommendation provides a theoretical basis for improving the quality and yield of tea leaves in summer and autumn.

Integrated transcriptome and metabolome analysis reveals the regulation of phlorizin synthesis in Lithocarpus polystachyus under nitrogen fertilization

BACKGROUND

Nitrogen (N) is essential for plant growth and development. In Lithocarpus polystachyus Rehd., a species known for its medicinal and food value, phlorizin is the major bioactive compound with pharmacological activity. Research has revealed a positive correlation between plant nitrogen (N) content and phlorizin synthesis in this species. However, no study has analyzed the effect of N fertilization on phlorizin content and elucidated the molecular mechanisms underlying phlorizin synthesis in L. polystachyus.

RESULTS

A comparison of the L. polystachyus plants grown without (0 mg/plant) and with N fertilization (25, 75, 125, 175, 225, and 275 mg/plant) revealed that 75 mg N/plant fertilization resulted in the greatest seedling height, ground diameter, crown width, and total phlorizin content. Subsequent analysis of the leaves using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) detected 150 metabolites, including 42 flavonoids, that were differentially accumulated between the plants grown without and with 75 mg/plant N fertilization. Transcriptomic analysis of the L. polystachyus plants via RNA sequencing revealed 162 genes involved in flavonoid biosynthesis, among which 53 significantly differed between the N-treated and untreated plants. Fertilization (75 mg N/plant) specifically upregulated the expression of the genes phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), and phlorizin synthase (PGT1) but downregulated the expression of trans-cinnamate 4-monooxygenase (C4H), shikimate O-hydroxycinnamoyltransferase (HCT), and chalcone isomerase (CHI), which are related to phlorizin synthesis. Finally, an integrated analysis of the transcriptome and metabolome revealed that the increase in phlorizin after N fertilization was consistent with the upregulation of phlorizin biosynthetic genes. Quantitative real-time PCR (qRT‒PCR) was used to validate the RNA sequencing data. Thus, our results indicated that N fertilization increased phlorizin metabolism in L. polystachyus by regulating the expression levels of the PAL, PGT1, 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase (C3'H), C4H, and HCT genes.

CONCLUSIONS

Our results demonstrated that the addition of 75 mg/plant N to L. polystachyus significantly promoted the accumulation of flavonoids, including phlorizin, and the expression of flavonoid synthesis-related genes. Under these conditions, the genes PAL, 4CL, and PGT1 were positively correlated with phlorizin accumulation, while C4H, CHI, and HCT were negatively correlated with phlorizin accumulation. Therefore, we speculate that PAL, 4CL, and PGT1 participate in the phlorizin pathway under an optimal N environment, regulating phlorizin biosynthesis. These findings provide a basis for improving plant bioactive constituents and serve as a reference for further pharmacological studies.

Comprehensive analysis of fresh tea (Camellia sinensis cv. Lingtou Dancong) leaf quality under different nitrogen fertilization regimes

Our study investigated the impact of nitrogen fertilization at 0, 150, 300, and 450 kg/ha on the non-volatile and volatile substances, as well as gene expression in fresh leaves from Lingtou tea plants. We found that applying nitrogen at 450 kg/ha notably increased total polyphenols (TPs) and free amino acids (AAs) while decreasing the TP to AA ratio (TP/AA) and total catechins (TC) contents. Chlorophyll, caffeine (CAF) and theanine accumulated to a greater extent with nitrogen application rates of 150, 300, and 450 kg/ha, respectively, six substances - TP, CAF, TC, theanine, epigallocatechin (EGC), and AA - as key contributors to the taste quality of LTDC. Additionally, five substances with variable importance in projections (VIP) ≥ 1 and odor activation values (OAV) ≥ 1, notably linalool and cis-linalool oxide (furanoid), significantly contributed to the tea's overall aroma. Furthermore, applying 300 kg/ha nitrogen upregulated the dihydroflavonol reductase (DFR)gene, likely causing catechin decrease.

Nitrogen Sources Reprogram Carbon and Nitrogen Metabolism to Promote Andrographolide Biosynthesis in Andrographis paniculata (Burm.f.) Nees Seedlings

Carbon (C) and nitrogen (N) metabolisms participate in N source-regulated secondary metabolism in medicinal plants, but the specific mechanisms involved remain to be investigated. By using nitrate (NN), ammonium (AN), urea (UN), and glycine (GN), respectively, as sole N sources, we found that N sources remarkably affected the contents of diterpenoid lactone components along with C and N metabolisms reprograming in Andrographis paniculata, as compared to NN, the other three N sources raised the levels of 14-deoxyandrographolide, andrographolide, dehydroandrographolide (except UN), and neoandrographolide (except AN) with a prominent accumulation of farnesyl pyrophosphate (FPP). These N sources also raised the photosynthetic rate and the levels of fructose and/or sucrose but reduced the activities of phosphofructokinase (PFK), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoenolpyruvate carboxylase (PEPC) and pyruvate dehydrogenase (PDH). Conversely, phosphoenolpyruvate carboxykinase (PEPCK) and malate enzyme (ME) activities were upregulated. Simultaneously, citrate, cis-aconitate and isocitrate levels declined, and N assimilation was inhibited. These results indicated that AN, UN and GN reduced the metabolic flow of carbohydrates from glycolysis into the TCA cycle and downstream N assimilation. Furthermore, they enhanced arginine and GABA metabolism, which increased C replenishment of the TCA cycle, and increased ethylene and salicylic acid (SA) levels. Thus, we proposed that the N sources reprogrammed C and N metabolism, attenuating the competition of N assimilation for C, and promoting the synthesis and accumulation of andrographolide through plant hormone signaling. To obtain a higher production of andrographolide in A. paniculata, AN fertilizer is recommended in its N management.

The effect of intercropping leguminous green manure on theanine accumulation in the tea plant: A metagenomic analysis

Intercropping is a widely recognised technique that contributes to agricultural sustainability. While intercropping leguminous green manure offers advantages for soil health and tea plants growth, the impact on the accumulation of theanine and soil nitrogen cycle are largely unknown. The levels of theanine, epigallocatechin gallate and soluble sugar in tea leaves increased by 52.87% and 40.98%, 22.80% and 6.17%, 22.22% and 29.04% in intercropping with soybean-Chinese milk vetch rotation and soybean alone, respectively. Additionally, intercropping significantly increased soil amino acidnitrogen content, enhanced extracellular enzyme activities, particularly β-glucosidase and N-acetyl-glucosaminidase, as well as soil multifunctionality. Metagenomics analysis revealed that intercropping positively influenced the relative abundances of several potentially beneficial microorganisms, including Burkholderia, Mycolicibacterium and Paraburkholderia. Intercropping resulted in lower expression levels of nitrification genes, reducing soil mineral nitrogen loss and N2 O emissions. The expression of nrfA/H significantly increased in intercropping with soybean-Chinese milk vetch rotation. Structural equation model analysis demonstrated that the accumulation of theanine in tea leaves was directly influenced by the number of intercropping leguminous green manure species, soil ammonium nitrogen and amino acid nitrogen. In summary, the intercropping strategy, particularly intercropping with soybean-Chinese milk vetch rotation, could be a novel way for theanine accumulation.

Root microbiota of tea plants regulate nitrogen homeostasis and theanine synthesis to influence tea quality

The flavor profile of tea is influenced not only by different tea varieties but also by the surrounding soil environment. Recent studies have indicated the regulatory role of soil microbes residing in plant roots in nutrient uptake and metabolism. However, the impact of this regulatory mechanism on tea quality remains unclear. In this study, we showed that a consortium of microbes isolated from tea roots enhanced ammonia uptake and facilitated the synthesis of theanine, a key determinant of tea taste. Variations were observed in the composition of microbial populations colonizing tea roots and the rhizosphere across different seasons and tea varieties. By comparing the root microorganisms of the high-theanine tea variety Rougui with the low-theanine variety Maoxie, we identified a specific group of microbes that potentially modulate nitrogen metabolism, subsequently influencing the theanine levels in tea. Furthermore, we constructed a synthetic microbial community (SynCom) mirroring the microbe population composition found in Rougui roots. Remarkably, applying SynCom resulted in a significant increase in the theanine content of tea plants and imparted greater tolerance to nitrogen deficiency in Arabidopsis. Our study provides compelling evidence supporting the use of root microorganisms as functional microbial fertilizers to enhance tea quality.

Influence of Organic and Inorganic Fertilizers on Tea Growth and Quality and Soil Properties of Tea Orchards' Top Rhizosphere Soil

Organic-based fertilizers have been ratified to be effective in ameliorating tea growth and the fertility of soil. However, the effect of integrated fertilization on tea growth and quality and the chemical properties of the soil in tea gardens are unclear. To address this, from 2020 to 2021, five different treatments were carried out in the greenhouse of the Tea Research Institute, Hangzhou, CAAS, including CK (control), NPK (chemical fertilizers), RC (rapeseed cake), NPK+B (chemical fertilizer + biochar), and NPK+RC, to investigate the effects of different fertilizations on soil chemistry and tea growth and quality. The results indicated that NPK+B and NPK+RC significantly improved the different amino acid and catechin concentrations in the young shoots, stems, and roots of the tea compared to the CK. The plant growth parameters, e.g., the plant height, no. of leaves, mid-stem girth, and fresh weights of stems and leaves, were significantly increased with integrated fertilization (NPK+B and NPK+RC) compared to the CK and solo organic and inorganic fertilizers. The chlorophyll contents (Chl a, Chl b, and Chl a+b) were generally higher with NPK+RC than with the CK (37%, 35%, and 36%), RC (14%, 26%, and 18%), and NPK (9%, 13%, and 11%) treatments. Integrated fertilization buffered the acidic soil of the tea garden and decreased the soil C:N ratio. NPK+RC also significantly increased the soil's total C (31% and 16%), N (43% and 31%), P (65% and 40%), available P (31% and 58%), K (70% and 25%), nitrate (504% and 188%), and ammonium (267% and 146%) concentrations compared to the CK and RC. The soil macro- (Mg and Ca) and micronutrients (Mn, Fe, Zn, and Cu) were significantly improved by the RC (100% and 72%) (49%, 161%, 112%, and 40%) and NPK+RC (88% and 48%) (47%, 75%, 45%, and 14%) compared to the CK. The chlorophyll contents and soil macro- and micronutrients were all significantly positively correlated with tea quality (amino acids and catechin contents) and growth. These results indicated that integrated fertilization improved the soil nutrient status, which is associated with the improvement of tea growth and quality. Thus, integrated nutrient management is a feasible tool for improving tea growth, quality, and low nutrient levels in the soil.

Analysis of Functional Single-Nucleotide Polymorphisms (SNPs) and Leaf Quality in Tea Collection under Nitrogen-Deficient Conditions

This study discusses the genetic mutations that have a significant association with economically important traits that would benefit tea breeders. The purpose of this study was to analyze the leaf quality and SNPs in quality-related genes in the tea plant collection of 20 mutant genotypes growing without nitrogen fertilizers. Leaf N-content, catechins, L-theanine, and caffeine contents were analyzed in dry leaves via HPLC. Additionally, the photochemical yield, electron transport efficiency, and non-photochemical quenching were analyzed using PAM-fluorimetry. The next generation pooled amplicon-sequencing approach was used for SNPs-calling in 30 key genes related to N metabolism and leaf quality. The leaf N content varied significantly among genotypes (p ≤ 0.05) from 2.3 to 3.7% of dry mass. The caffeine content varied from 0.7 to 11.7 mg g-1, and the L-theanine content varied from 0.2 to 5.8 mg g-1 dry leaf mass. Significant positive correlations were detected between the nitrogen content and biochemical parameters such as theanine, caffeine, and most of the catechins. However, significant negative correlations were observed between the photosynthetic parameters (Y, ETR, Fv/Fm) and several biochemical compounds, including rutin, Quercetin-3-O-glucoside, Kaempferol-3-O-rutinoside, Kaempferol-3-O-glucoside, Theaflavin-3'-gallate, gallic acid. From our SNP-analysis, three SNPs in WRKY57 were detected in all genotypes with a low N content. Moreover, 29 SNPs with a high or moderate effect were specific for #316 (high N-content, high quality) or #507 (low N-content, low quality). The use of a linear regression model revealed 16 significant associations; theaflavin, L-theanine, and ECG were associated with several SNPs of the following genes: ANSa, DFRa, GDH2, 4CL, AlaAT1, MYB4, LHT1, F3'5'Hb, UFGTa. Among them, seven SNPs of moderate effect led to changes in the amino acid contents in the final proteins of the following genes: ANSa, GDH2, 4Cl, F3'5'Hb, UFGTa. These results will be useful for further evaluations of the important SNPs and will help to provide a better understanding of the mechanisms of nitrogen uptake efficiency in tree crops.

Nitrogen transport and assimilation in tea plant (Camellia sinensis): a review

Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.

Effects of Different Nitrogen Forms on Blackberry Fruit Quality

To study the optimal form of nitrogen (N) application and to determine the best harvest date for blackberries, different N fertilizers were applied during the critical growth period of blackberry plants. The results showed that NH₄⁺-N significantly improved the appearance of blackberry fruits, including their size, firmness, and color, and promoted the accumulation of soluble solids, sugars, anthocyanin, ellagic acid, and vitamin C (VC), while fruit treated with NO₃^--N accumulated more flavonoids and organic acids and had improved antioxidant capacity. In addition, the fruit size, firmness, and color brightness decreased with the harvest period. While the contents of sugars, anthocyanin, ellagic acid, flavonoids, and VC were higher in the early harvests and then decreased as the season progressed, the total antioxidant capacity and DPPH radical scavenging capacity increased. In all, application of NH₄⁺-N is recommended, as it is more beneficial to fruit appearance, taste, and nutritional quality. Harvests in the early stage help to obtain a good fruit appearance, while harvests in the middle and later stages are more beneficial to fruit taste and quality. This study may help growers to determine the best fertilization scheme for blackberries and choose the appropriate harvest time according to their needs.

Magnesium promotes tea plant growth via enhanced glutamine synthetase-mediated nitrogen assimilation

Acidic tea (Camellia sinensis) plantation soil usually suffers from magnesium (Mg) deficiency, and as such, application of fertilizer containing Mg can substantially increase tea quality by enhancing the accumulation of nitrogen (N)-containing chemicals such as amino acids in young tea shoots. However, the molecular mechanisms underlying the promoting effects of Mg on N assimilation in tea plants remain unclear. Here, both hydroponic and field experiments were conducted to analyze N, Mg, metabolite contents, and gene expression patterns in tea plants. We found that N and amino acids accumulated in tea plant roots under Mg deficiency, while metabolism of N was enhanced by Mg supplementation, especially under a low N fertilizer regime. 15N tracing experiments demonstrated that assimilation of N was induced in tea roots following Mg application. Furthermore, weighted gene correlation network analysis (WGCNA) analysis of RNA-seq data suggested that genes encoding glutamine synthetase isozymes (CsGSs), key enzymes regulating N assimilation, were markedly regulated by Mg treatment. Overexpression of CsGS1.1 in Arabidopsis (Arabidopsis thaliana) resulted in a more tolerant phenotype under Mg deficiency and increased N assimilation. These results validate our suggestion that Mg transcriptionally regulates CsGS1.1 during the enhanced assimilation of N in tea plant. Moreover, results of a field experiment demonstrated that high Mg and low N had positive effects on tea quality. This study deepens our understanding of the molecular mechanisms underlying the interactive effects of Mg and N in tea plants while also providing both genetic and agronomic tools for future improvement of tea production.

Physiological and Morphological Responses of Blackberry Seedlings to Different Nitrogen Forms

Blackberries are an emerging third-generation fruit that are popular in Europe, and specific nitrogen (N) supply is an important factor affecting their growth and development. To study the optimal N fertilizer for blackberry seedlings, no N (CK), nitrate (NO₃^-)-N, ammonium (NH₄⁺)-N and urea were applied to one-year-old 'Ningzhi 4' blackberry plants at a key growth period (from May to August) to explore the effects of different N forms on the physiological characteristics. Correlation and principal component analysis were used to determine the relationships between various indexes. Ammonium (NH₄⁺) or urea-fed plants had a better growth state, showed a greater plant height, biomass, SPAD values and enhanced antioxidant enzyme activities and photosynthesis. In addition, NH₄⁺ was beneficial to the accumulation of sugars and amino acids in leaves and roots, and promoted the transport of auxin and cytokinin to leaves. NO₃^- significantly inhibited root growth and increased the contents of active oxygen, malondialdehyde and antioxidants in roots. Correlation and principal component analysis showed that growth and dry matter accumulation were closely related to the antioxidant system, photosynthetic characteristics, amino acids and hormone content. Our study provides a new idea for N regulation mechanism of blackberry and proposes a scientific fertilization strategy.

Differences in transcriptomic and metabolomic analyses of metabolites of shoots on tea plants of different ages and relevant regulatory network

To investigate differences in fresh leaves of tea plants at different ages in gene expression, metabolism, and dried tea quality, and to provide references to a deep exploration on metabolite differential accumulation of fresh leaves of tea plants at different ages as well as the regulation mechanism, two groups of fresh leaves from tea plants at different ages (group JP: 20-, 200-, and 1,200-year tea plants; group YX: 50-, 100-, and 400-year tea plants) were chosen as materials, and their differences in gene expression, metabolites, and metabolic regulatory network were investigated by transcriptomics and metabolomics. A total of 12,706 differentially expressed genes (DEGs) were screened from the fresh tea leaves in the JP group, of which tea-20 vs. tea-200 had the largest number of DEGs, up to 9,041 (4,459 down-regulated genes, 4,582 up-regulated genes). A total of 644 common genes in the fresh leaves of three different ages of tea plants in the JP group were differentially expressed. A total of 8,971 DEGs were screened from the fresh leaf samples of tea plants in the YX group, of which the number of DEGs obtained in the tea-50 vs. tea-400 comparison combination was the largest with a total of 3,723 (1,722 up-regulated genes and 2,001 down-regulated genes). A total of 147 common genes were differentially expressed in the fresh leaves of three different tree ages in the YX group. The pathway enrichment analysis showed that most up-regulated DEGs and their related metabolic pathways were similar in the two groups, and that the metabolic pathways of common significant enrichment included flavonoid biosynthesis, phenylpropane biosynthesis, carbon metabolism, amino acid biosynthesis, and plant pathogen interaction. The metabolomics results showed that 72 and 117 different metabolites were screened from the JP and YX groups, respectively. Most of the different metabolites in the two groups were flavonoids, phenolic acids, amino acids, and their derivatives. Among them, the number of down-regulated flavonoids in older tea plants is generally higher than the number of up-regulated flavonoids. Moreover, according to the sensory evaluation results of dried tea of fresh leaves from tea plants of different ages, tea-1200 and tea-400 showed the highest sensory evaluation scores in their groups. With increase in plant age, the fragrance of the tea was more elegant, and it changed from a dense scent to a faint scent; the tea tasted sweet and its freshness increased, while the sense of astringency was weakened and the concentration declined. Therefore, the quality difference of tea of different tree ages is mainly related to secondary metabolic pathways such as the flavonoid biosynthesis pathway. With increase in tea age, a large number of gene expression in the flavonoid biosynthesis pathway is down-regulated, which reduces the content of bitter flavonoid substances in fresh leaves and makes tea soup more mellow.

Overexpression of CsATG3a improves tolerance to nitrogen deficiency and increases nitrogen use efficiency in arabidopsis

Nitrogen (N) is a major nutrition element for tea plant. However, application of high levels of N negatively causes environmental problems. Therefore, improved N use efficiency (NUE) of tea plant will be highly desirable and crucial for sustainable tea cultivation. Autophagy plays a central role in N recycling and holds potential to improve N utilization, and many AuTophaGy-related genes (ATGs) are involved in the autophagy process. Here, CsATG3a was identified from Camellia sinensis, and the functions involved in N utilization was characterized in arabidopsis (Arabidopsis thaliana). The transcript level of CsATG3a in tea leaves increases with their maturity. Relative to the wild type (WT) arabidopsis, two CsATG3a-overexpressing (CsATG3a-OE) lines exhibited improved vegetative growth, delayed reproductive stage, and upregulated expression of AtATGs (AtATG3, AtATG5 and AtATG8b) in a low N (LN) hydroponic condition. The expression levels of AtNRT1.1, AtNRT2.1, AtNRT2.2, AtAMT1.1 and AtAMT1.3 for N uptake and transport in roots were all significantly higher in CsATG3a-OE lines compared with those in the WT under LN. Meanwhile, the overexpression of CsATG3a in arabidopsis also increased N and dry matter allocation into both rosette leaves and roots under LN. Additionally, compared with WT, improved HI (harvest index), NHI (N harvest index), NUtE (N utilization efficiency) and NUE (N use efficiency) of CsATG3a-OE lines were further confirmed in a low-N soil cultured experiment. Together, these results concluded that CsATG3a is involved in N recycling and enhances tolerance to LN, indicating that CsATG3a holds potential promise to improve NUE in tea plant.

Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea

Tea, which is processed by the tender shoots or leaves of tea plant (Camellia sinensis), is one of the most popular nonalcoholic beverages in the world and has numerous health benefits for humans. Along with new progress in biotechnologies, the refined chromosome-scale reference tea genomes have been achieved, which facilitates great promise for the understanding of fundamental genomic architecture and evolution of the tea plants. Here, we summarize recent achievements in genome sequencing in tea plants and review the new progress in origin and evolution of tea plants by population sequencing analysis. Understanding the genomic characterization of tea plants is import to improve tea quality and accelerate breeding in tea plants.

Integrated untargeted metabolome, full-length sequencing, and transcriptome analyses reveal insights into the fruit quality at different harvest times of Chaenomeles speciosa

Chaenomeles speciosa fruit is a homologous medicine and food plant with a long history of multiple uses. It could be harvested near maturity and last for a long time. However, the optimal harvest strategy of Chaenomeles speciosa for various uses is currently unavailable. Here, untargeted metabolome at different harvest times during maturation was investigated for the first time, and 896 metabolites, including sugars, organic acids, amino acids, and phenylpropanoids, were identified. Optimal harvesting methods were proposed for different purposes. During the early maturation stages (before 105 days after full bloom), Ch. speciosa fruit could be harvested as Chinesemedicine. Whereas as snacks and food, Ch. speciosa fruit might be harvested at late maturity (after 120 days after full bloom). In addition, the overall network was revealed by integrating full-length Iso-seq and transcriptomics (RNA-seq) to investigate the association between quality-associated metabolites and Chaenomeles speciosa fruit gene expression during maturation. A few putative genes were captured via screening, dissecting and correlation analysis with the quality-associated metabolites (including d-glucose, catechin, gallocatechin, and succinic acid). Overall, in addition to providing a harvesting strategy for food and medicine, we also investigated the metabolism and gene expression pattern of Chaenomeles speciosa fruit during maturation. This comprehensive data and analyses laid the foundation for further investigating potential regulatory mechanisms during harvest and provided a new possibility for its development and utilization.

Integrative physiological, metabolomic and transcriptomic analysis reveals nitrogen preference and carbon and nitrogen metabolism in blackberry plants

Nitrogen (N) is an indispensable element for plant growth and development. To understand the regulation of underlying carbon (C) and N metabolism in blackberry plants, we performed integrated analyses of the physiology, metabolome and transcriptome. Blackberry plants were subjected to no N, nitrate (NO₃⁻)-N, ammonium (NH₄⁺)-N and urea treatments. Our results showed that the NH₄⁺-N treatment yielded higher values for the biomass, chlorophyll, antioxidants, N contents and antioxidant enzyme activities, as well as lower levels of free radicals and the C/N ratio compared with other treatments. Transcriptome analysis showed that different N forms significantly affected photosynthesis, flavonoid biosynthesis and the TCA cycle. Metabolome analysis indicated that the levels of lipids, carbohydrates, flavonoids and amino acids were markedly changed under different N treatments. Integrated transcriptomic and metabolomic data revealed that amino acids, including proline, arginine, L-isoleucine, L-aspartate, threonine, and L-glutamate, played important roles in maintaining normal plant growth by regulating N metabolism and amino acid metabolism. Overall, blackberry plants preferentially take up NH₄⁺-N. Under the NH₄⁺-N treatment, N assimilation was stronger, flavonoid biosynthesis was decreased, and the promoting influence of NH₄⁺-N on N metabolism was better than that of NO₃⁻-N. However, the NO₃⁻-N treatment enhanced the C/N ratio, accelerated the process of C metabolism and increased the synthesis of flavonoids, thereby accelerating the flow of N metabolism to C metabolism. These results provide deeper insight into coordinating C and N metabolism and improving N use efficiency in blackberry plants.

Soil metagenomic analysis on changes of functional genes and microorganisms involved in nitrogen-cycle processes of acidified tea soils

Nitrogen (N) is the first essential nutrient for tea growth. However, the effect of soil acidification on soil N cycle and N forms in tea plantation are unclear. In this study, the nitrogen contents, soil enzyme activity and N mineralization rate in acidified soil of tea plantation were measured. Moreover, the effects of soil acidification on N cycling functional genes and functional microorganisms were explored by soil metagenomics. The results showed that the NH₄ ⁺-N, available N and net N mineralization rate in the acidified tea soil decreased significantly, while the NO₃ ^--N content increased significantly. The activities of sucrase, protease, catalase and polyphenol oxidase in the acidified tea soil decreased significantly. The abundance of genes related to ammonification, dissimilatory N reduction, nitrification and denitrification pathway in the acidified tea soil increased significantly, but the abundance of functional genes related to glutamate synthesis and assimilatory N reduction pathway were opposite. In addition, the abundance of Proteobacteria, Actinobacteria, Chloroflexi, Nitrospirae, Actinomadura, Nitrospira etc. microorganisms related to nitrification, denitrification and pathogenic effect increased significantly in the acidified tea soil. The correlation results showed that soil pH and N forms were correlated with soil enzyme activity, N cycling function genes and microbial changes. In conclusion, soil acidification results in significant changes in enzyme activity, gene abundance and microorganism involved in various N cycle processes in acidified tea soil, which leads to imbalance of soil N form ratio and is not conducive to N transformation and absorption of tea trees.

Effects of pruning on mineral nutrients and untargeted metabolites in fresh leaves of Camellia sinensis cv. Shuixian

Pruning is an important strategy for increasing tea production. However, the effects of pruning on tea quality are not well understood. In this study, tea leaves were collected from Wuyi Mountain for both ionomic and metabolomic analyses. A total of 1962 and 1188 fresh tea leaves were respectively collected from pruned and unpruned tea plants sampled across 350 tea plantations. Ionomic profiles of fresh tea leaves varied significantly between pruned and unpruned sources. For tea plants, pruning was tied to decreases in the concentrations of mobile elements, such as nitrogen (N), phosphorus (P), potassium (K) and magnesium (Mg), and dramatic increases in the concentrations of the immobile ions calcium (Ca), aluminum (Al), manganese (Mn), boron (B) and cobalt (Co). Clustering and heatmap analysis showed that pruning also affected tea leaf metabolism. Among 85 metabolites that were significantly impacted by pruning, 30 were identified through random forest analysis as characteristic differential metabolites with a prediction rate of 86.21%. Redundancy analysis showed that pruning effects on mineral nutrient concentrations accounted for 25.54% of the variation in characteristic metabolites between treatments, with the highest contributions of 6.64% and 3.69% coming from Ca and Mg, respectively. In correlation network analysis, Ca and Mg both exhibited close, though opposing correlations with six key metabolites, including key quality indicators 1,3-dicaffeoylquinic acid and 2-O-caffeoyl arbutin. In summary, large scale sampling over hundreds of tea plantations demonstrated that pruning affects tea quality, mainly through influences on leaf mineral composition, with Ca and Mg playing large roles. These results may provide a solid scientific basis for improved management of high-quality tea plantations.

Metabolome and RNA-seq Analysis of Responses to Nitrogen Deprivation and Resupply in Tea Plant (Camellia sinensis) Roots

Nitrogen (N) is an important contributor in regulating plant growth and development as well as secondary metabolites synthesis, so as to promote the formation of tea quality and flavor. Theanine, polyphenols, and caffeine are important secondary metabolites in tea plant. In this study, the responses of Camellia sinensis roots to N deprivation and resupply were investigated by metabolome and RNA-seq analysis. N deficiency induced content increase for most amino acids (AAs) and reduction for the remaining AAs, polyphenols, and caffeine. After N recovery, the decreased AAs and polyphenols showed a varying degree of recovery in content, but caffeine did not. Meanwhile, theanine increased in content, but its related synthetic genes were down-regulated, probably due to coordination of the whole N starvation regulatory network. Flavonoids-related pathways were relatively active following N stress according to KEGG enrichment analysis. Gene co-expression analysis revealed TCS2, AMT1;1, TAT2, TS, and GOGAT as key genes, and TFs like MYB, bHLH, and NAC were also actively involved in N stress responses in C. sinensis roots. These findings facilitate the understanding of the molecular mechanism of N regulation in tea roots and provide genetic reference for improving N use efficiency in tea plant.

Hormonal regulation of health-promoting compounds in tea (Camellia sinensis L.)

Tea is the most frequently consumed natural beverage across the world produced with the young leaves and shoots of the evergreen perennial plant Camellia sinensis (L.) O. Kuntze. The expanding global appeal of tea is partly attributed to its health-promoting benefits such as anti-inflammation, anti-cancer, anti-allergy, anti-hypertension, anti-obesity, and anti- SARS-CoV-2 activity. The many advantages of healthy tea intake are linked to its bioactive substances such as tea polyphenols, flavonoids (catechins), amino acids (theanine), alkaloids (caffeine), anthocyanins, proanthocyanidins, etc. that are produced through secondary metabolic pathways. Phytohormones regulate secondary metabolite biosynthesis in a variety of plants, including tea. There is a strong hormonal response in the biosynthesis of polyphenols, catechins, theanine and caffeine in tea under control and perturbed environmental conditions. In addition to the impact of preharvest plant hormone manipulation on green tea quality, changes in hormones of postharvest tea also regulate quality-related metabolites in tea. In this review, we discuss the health benefits of major tea constituents and the role of various plant hormones in improving the endogenous levels of these compounds for human health benefits. The fact that the ratio of tea polyphenols to amino acids and the concentrations of tea components are changed by environmental conditions, most notably by climate change-associated variables, the selection and usage of optimal hormone combinations may aid in sustaining tea quality, and thus can be beneficial to both consumers and producers.

Recent advances in proteomics and metabolomics in plants

Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.

Regulation of biosynthesis of the main flavor-contributing metabolites in tea plant (Camellia sinensis): A review

In the process of adapting to the environment, tea plants (Camellia sinensis) endow tea with unique flavor and health functions, which should be attributed to secondary metabolites, including catechins, L-theanine, caffeine and terpene volatiles. Since the content of these flavor-contributing metabolites are mainly determined by the growth of tea plant, it is very important to understand their alteration and regulation mechanisms. In the present work, we first summarize the distribution, change characteristics of the main flavor-contributing metabolites in different cultivars, organs and under environmental stresses of tea plant. Subsequently, we discuss the regulating mechanisms involved in the biosynthesis of these metabolites based on the existing evidence. Finally, we propose the remarks and perspectives on the future study relating flavor-contributing metabolites. This review would contribute to the acceleration of research on the characteristic secondary metabolites and the breeding programs in tea plants.

Directed Accumulation of Nitrogen Metabolites through Processing Endows Wuyi Rock Tea with Singular Qualities

The execution of specific processing protocols endows Wuyi rock tea with distinctive qualities produced through signature metabolic processes. In this work, tea leaves were collected before and after each of three processing stages for both targeted and untargeted metabolomic analysis. Metabolic profiles of processing stages through each processing stage of rotation, pan-firing and roasting were studied. Overall, 614 metabolites were significantly altered, predominantly through nitrogen- enriching (N) pathways. Roasting led to the enrichment of 342 N metabolites, including 34 lipids, 17 organic acids, 32 alkaloids and 25 amino acids, as well as secondary derivatives beneficial for tea quality. This distinctive shift towards enrichment of N metabolites strongly supports concluding that this directed accumulation of N metabolites is how each of the three processing stages endows Wuyi rock tea with singular quality.

The Transcriptome and Metabolome Reveal the Potential Mechanism of Lodging Resistance in Intergeneric Hybrids between Brassica napus and Capsella bursa-pastoris

Lodging is one of the main reasons for the reduction in seed yield and is the limitation of mechanized harvesting in B. napus. The dissection of the regulatory mechanism of lodging resistance is an important goal in B. napus. In this study, the lodging resistant B. napus line, YG689, derived from the hybridization between B. napus cv. Zhongyou 821 (ZY821) and Capsella bursa-pastoris, was used to dissect the regulation mechanism of hard stem formation by integrating anatomical structure, transcriptome and metabolome analyses. It was shown that the lignocellulose content of YG689 is higher than that of ZY821, and some differentially expressed genes (DEGs) involved in the lignocellulose synthesis pathway were revealed by transcriptome analyses. Meanwhile, GC–TOF–MS and UPLC–QTOF–MS identified 40, 54, and 31 differential metabolites in the bolting stage, first flower stage, and the final flower stage. The differential accumulation of these metabolites might be associated with the lignocellulose biosynthesis in B. napus. Finally, some important genes that regulate the metabolic pathway of lignocellulose biosynthesis, such as BnaA02g18920D, BnaA10g15590D, BnaC05g48040D, and NewGene_216 were identified in B. napus through the combination of transcriptomics and metabolomics data. The present results explored the potential regulatory mechanism of lignocellulose biosynthesis, which provided a new clue for the breeding of B. napus with lodging resistance in the future.

Theanine metabolism and transport in tea plants (Camellia sinensis L.): advances and perspectives

Theanine, a tea plant-specific non-proteinogenic amino acid, is the most abundant free amino acid in tea leaves. It is also one of the most important quality components of tea because it endows the "umami" taste, relaxation-promoting, and many other health benefits of tea infusion. Its content in tea leaves is directly correlated with the quality and price of green tea. Theanine biosynthesis primarily occurs in roots and is transported to new shoots in tea plants. Recently, great advances have been made in theanine metabolism and transport in tea plants. Along with the deciphering of the genomic sequences of tea plants, new genes in theanine metabolic pathway were discovered and functionally characterized. Theanine transporters were identified and were characterized on the affinity for: theanine, substrate specificity, spatiotemporal expression, and the role in theanine root-to-shoot transport. The mechanisms underlying the regulation of theanine accumulation by: cultivars, seasons, nutrients, and environmental factors are also being rapidly uncovered. Transcription factors were identified to be critical regulators of theanine biosynthesis. In this review, we summarize the progresses in theanine: biosynthesis, catabolism, and transport processes. We also discuss the future studies on theanine in tea plants, and application of the knowledge to crops to synthesize theanine to improve the health-promoting quality of non-tea crops.

Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis

Specialized metabolites not only play important roles in biotic and abiotic stress adaptation of tea plants (Camellia sinensis (L.) O. Kuntze) but also contribute to the unique flavor of tea, the most important nonalcoholic beverage. However, the molecular networks and major genes that regulate specialized metabolites in tea plants are not well understood. Here, we constructed a population-level pan-transcriptome of the tea plant leaf using second-leaf transcriptome data from 134 accessions to investigate global expression differences in the population, expression presence or absence variations (ePAVs), and differentially expressed genes (DEGs) between pure Camellia sinensis var. assamica (CSA) and pure Camellia sinensis var. sinensis (CSS) accessions. Next, we used a genome-wide association study, a quantitative trait transcript study, and a transcriptome-wide association study to integrate genotypes, accumulation levels of specialized metabolites, and expression levels of pan-transcriptome genes to identify candidate regulatory genes for flavor-related metabolites and to construct a regulatory network for specialized metabolites in tea plants. The pan-transcriptome contains 30 482 expressed genes, 4940 and 5506 of which were newly annotated from a de novo transcriptome assembly without a reference and a genome reference-based assembly, respectively. DEGs and ePAVs indicated that CSA and CSS were clearly differentiated at the population transcriptome level, and they were closely related to abiotic tolerance and secondary metabolite synthesis phenotypes of CSA and CSS based on gene annotations. The regulatory network contained 212 specialized metabolites, 3843 candidate genes, and 3407 eQTLs, highlighting many pleiotropic candidate genes, candidate gene-rich eQTLs, and potential regulators of specialized metabolites. These included important transcription factors in the AP2/ERF-ERF, MYB, WD40, and bHLH families. CsTGY14G0001296, an ortholog of AtANS, appeared to be directly related to variation in proanthocyanins in the tea plant population, and the CsTGY11G0002074 gene encoding F3'5'H was found to contribute to the biased distribution of catechins between pure CSAs and pure CSSs. Together, these results provide a new understanding of the metabolite diversity in tea plants and offer new insights for more effective breeding of better-flavored tea varieties.

Updates on the chemistry, processing characteristics, and utilization of tea flavonoids in last two decades (2001-2021)

Tea flavonoids are widely recognized as critical flavor contributors and crucial health-promoting bioactive compounds, and have long been the focus of research worldwide in food science. The aim of this review paper is to summarize the major progress in tea flavonoid chemistry, their dynamics of constituents and concentrations during tea processing as well as storage, and their health functions studied between 2001 and 2021. Moreover, the utilization of tea flavonoids in the human body has also been discussed for a detailed understanding of their uptake, metabolism, and interaction with the gut microbiota. Many novel tea flavonoids have been identified, including novel A- and B-ring substituted flavan-3-ol derivatives, condensed and oxidized flavan-3-ol derivatives, and glycosylated and methylated flavonoids, and are found to be closely associated with the characteristic color, flavor, and health benefits of tea. Flavoalkaloids exist widely in various teas, particularly 8-C N-ethyl-2-pyrrolidinone-substituted flavan-3-ols. Tea flavonoids behave significantly difference in constituents and concentrations depending on tea cultivars, plantation conditions, multiple stresses, the tea-specified manufacturing steps, and even the long-term storage period. Tea flavonoids exhibit multiple health-promoting effects, particularly their anti-inflammatory in alleviating metabolic syndromes. Interaction of tea flavonoids with the gut microbiota plays vital roles in their health function.

Accumulation of Amino Acids and Flavonoids in Young Tea Shoots Is Highly Correlated With Carbon and Nitrogen Metabolism in Roots and Mature Leaves

The quality of tea product and the metabolism of quality-related compounds in young shoots are significantly affected by the nitrogen(N) supply. However, little is known of the metabolic changes that take place in tea roots and mature leaves under different supplies, which has a large effect on the accumulation of quality-related compounds in young shoots. In this study, young shoots, mature leaves, and roots under different N conditions were subjected to metabolite profiling using gas chromatography and ultraperformance liquid chromatography, coupled with quadrupole time-of-flight mass spectrometry. The contents of free amino acids (e.g., theanine and glutamate) involved in N metabolism were significantly greater under high N than under low N, while a high N supply reduced soluble sugars (e.g., glucose) in all three tissues. Organic acids (e.g., malate, fumarate, α-ketoglutatare, and succinate) involved in tricarboxylic acid cycle remarkably increased as the nitrogen supply increased, which confirms that carbon (C) allocation was restricted by increasing the nitrogen supply, especially in mature leaves. RT-PCR results indicated that gene expression related to nitrogen assimilation significantly increased in roots with increasing nitrogen supply, which had a significant positive relationship with the level of free amino acids in young shoots. In addition, the expression of most genes involved in flavonoid synthesis was significantly upregulated under conditions of low nitrogen supply relative to high nitrogen supply in young shoot and roots. These data suggest that enhanced assimilation of N in tea roots and the coordinated regulation of C (sugars, organic acids, and flavonoids) and N(amino acids) in mature leaves can lead to a high accumulation of amino acids in young shoots. Furthermore, as the N supply increased, more C was partitioned into compounds containing N in mature leaves and roots, resulting in a decrease in flavonoids in young shoots. In conclusion, the accumulation of amino acids and flavonoids in young tea shoots is highly correlated with carbon and nitrogen metabolism in roots and mature leaves.

The GC-TOF/MS-based Metabolomic analysis reveals altered metabolic profiles in nitrogen-deficient leaves and roots of tea plants (Camellia sinensis)

BACKGROUND

Nitrogen (N) fertilizer is commonly considered as one of the most important limiting factors in the agricultural production. As a result, a large amount of N fertilizer is used to improve the yield in modern tea production. Unfortunately, the large amount of N fertilizer input has led to increased plant nitrogen-tolerance and decreased amplitude of yield improvement, which results in significant N loss, energy waste and environment pollution. However, the effects of N-deficiency on the metabolic profiles of tea leaves and roots are not well understood.

RESULTS

In this study, seedlings of Camellia sinensis (L.) O. Kuntze Chunlv 2 were treated with 3 mM NH4NO3 (Control) or without NH4NO3 (N-deficiency) for 4 months by sandy culture. The results suggested that N-deficiency induced tea leaf chlorosis, impaired biomass accumulation, decreased the leaf chlorophyll content and N absorption when they were compared to the Control samples. The untargeted metabolomics based on GC-TOF/MS approach revealed a discrimination of the metabolic profiles between N-deficient tea leaves and roots. The identification and classification of the altered metabolites indicated that N deficiency upregulated the relative abundances of most phenylpropanoids and organic acids, while downregulated the relative abundances of most amino acids in tea leaves. Differentially, N-deficiency induced the accumulation of most carbohydrates, organic acids and amino acids in tea roots. The potential biomarkers screened in N-deficient leaves compared to Control implied that N deficiency might reduce the tea quality. Unlike the N-deficient leaves, the potential biomarkers in N-deficient roots indicated an improved stress response might occur in tea roots.

CONCLUSIONS

The results demonstrated N deficiency had different effects on the primary and secondary metabolism in tea leaves and roots. The findings of this study will facilitate a comprehensive understanding of the N-deficient tea plants and provide a valuable reference for the optimized N nutrient management and the sustainable development in the tea plantations.

Influence of different nitrogen sources on carbon and nitrogen metabolism and gene expression in tea plants (Camellia sinensis L.)

Nitrogen plays an important role in plant growth and development, with different nitrogen forms also having an impact on carbon/nitrogen metabolism. Unlike most plants, tea plants prefer ammonium over nitrate. In this paper, we focused on how different nitrogen sources regulate the carbon/nitrogen metabolism in tea plants. Tea seedlings of 'Longjing 43' were cultivated hydroponically in four different solutions (zero-nitrogen, only NH₄⁺, only NO₃^- and mixed nitrogen (NH₄⁺: NO₃^- = 1:1). We analyzed characteristic components of tea plants and related genes in carbon and nitrogen metabolism. Tea polyphenols and catechins representing carbon pool, increased when NO₃^- was supplied as the nitrogen source, and similar findings were recorded in the zero-nitrogen treatment. The expression of most catechins biosynthesis-related genes was up regulated under NO₃^- and zero-N treatment, that was associated with tea polyphenols and catechins changes. Compared with NO₃^- as the nitrogen source, NH₄⁺ and mixed nitrogen treatments had a positive effect on the accumulation of amino acids, especially theanine, glutamate and arginine, and these components contribute to the freshness flavor of tea. The expression of ammonium-assimilation genes was also up-regulated with NH₄⁺ supply. Under mixed nitrogen treatment, the ratio of total polyphenols to free amino acids (PP/AA) was between sole NH₄⁺ and NO₃^- supply. Therefore, compared with single nitrogen source, carbon and nitrogen metabolism of tea plant was more balanced under mixed nitrogen treatment. The results suggested that NO₃^- as the nitrogen source promoted the biosynthesis of catechins enriching the carbon pool, whereas NH₄⁺ supply was more conducive to nitrogen metabolism, indicating that different nitrogen sources could affect the carbon and nitrogen balance.

Integrating transcriptome and physiological analyses to elucidate the essential biological mechanisms of graphene phytotoxicity of alfalfa (Medicago sativa L.)

The phytotoxicity of nanoparticles has attracted considerable interest, given the broad applications of nanomaterials in different fields. Alfalfa (Medicago sativa L.) is a major forage crop grown worldwide with a high protein content. The molecular regulation mechanisms involved in nanomaterial-treated alfalfa were examined in this research. In our lab, 18 cDNA libraries of Golden Empress (GE) and Bara 310SC (SC) under control (CK), middle (10 g kg^-1)- and high (20 g kg^-1)-graphene stress treatments were constructed in 2019. All clean reads were matched to the reference Medicago_truncatula genome, the mapping ratio was higher than 50%, and a total of 3946 differentially expressed genes (DEGs) were obtained. The number of DEGs that reflect transcriptional activity is proportional to the degree of stress. For example, 1241/610 and 1794/1422 DEGs were identified as significant in the leaves of GE/SC under mid- and high-graphene treatment, respectively. Furthermore, GO analysis of the DEGs annotated in some significant biochemical process terms included 'response to abiotic stimulus', 'oxidation-reduction process', 'protein kinase activity', and 'oxidoreductase activity'. KEGG pathway analysis of the DEGs revealed strongly mediated graphene-responsive genes in alfalfa mainly linked to the 'biosynthesis of amino acids', 'isoflavonoid biosynthesis', 'linoleic acid metabolism', and 'phenylpropanoid biosynthesis' pathways. In addition, hundreds of DEGs, including photosynthetic, antioxidant enzyme, nitrogen metabolism, and metabolic sucrose and starch genes, have been identified as potentially involved in the response to graphene. Physiological findings revealed that enzymes related to the metabolism of nitrogen play a crucial role in the adaptation of graphene stress to alfalfa. Ultimately, in response to graphene stress, a preliminary regulatory mechanism was proposed for the self-protective mechanism of alfalfa, which helps to explain the phytotoxicity of the molecular mechanism of nanoparticle-treated crops.

Nitrogen-Regulated Theanine and Flavonoid Biosynthesis in Tea Plant Roots: Protein-Level Regulation Revealed by Multiomics Analyses

Theanine and flavonoids (especially proanthocyanidins) are the most important and abundant secondary metabolites synthesized in the roots of tea plants. Nitrogen promotes theanine and represses flavonoid biosynthesis in tea plant roots, but the underlying mechanism is still elusive. Here, we analyzed theanine and flavonoid metabolism in tea plant roots under nitrogen deficiency and explored the regulatory mechanism using proteome and ubiquitylome profiling together with transcriptome data. Differentially expressed proteins responsive to nitrogen deficiency were identified and found to be enriched in flavonoid, nitrogen, and amino acid metabolism pathways. The proteins responding to nitrogen deficiency at the transcriptional level, translational level, and both transcriptional and translational levels were classified. Nitrogen-deficiency-responsive and ubiquitinated proteins were further identified. Our results showed that most genes encoding enzymes in the theanine synthesis pathway, such as CsAlaDC, CsGDH, and CsGOGATs, were repressed by nitrogen deficiency at transcriptional and/or protein level(s). While a large number of enzymes in flavonoid metabolism were upregulated at the transcriptional and/or translational level(s). Importantly, the ubiquitylomic analysis identified important proteins, especially the hub enzymes in theanine and flavonoid biosynthesis, such as CsAlaDC, CsTSI, CsGS, CsPAL, and CsCHS, modified by ubiquitination. This study provided novel insights into the regulation of theanine and flavonoid biosynthesis and will contribute to future studies on the post-translational regulation of secondary metabolism in tea plants.

Multiomics Analysis Reveals New Insights into the Apple Fruit Quality Decline under High Nitrogen Conditions

Excessive application of nitrogen (N) fertilizer is common in Chinese apple production. High N reduced the contents of soluble sugar and total flavonoids by 16.05 and 19.01%, respectively, resulting in poor fruit quality. Moreover, high N increased the total N and decreased the total C and C/N ratio of apple fruits. On the basis of the transcriptomic, proteomic, and metabolomic analyses, the global network was revealed. High N inhibited the accumulation of carbohydrates (sucrose, glucose, and trehalose) and flavonoids (rhamnetin-3-O-rutinoside, rutin, and trihydroxyisoflavone-7-O-galactoside) in fruits, and more C skeletons were used to synthesize amino acids and their derivatives (especially low C/N ratio, e.g., arginine) to be transferred to N metabolism. This study revealed new insights into the decline in soluble sugar and flavonoids caused by high N, and hub genes (MD07G1172700, MD05G1222800, MD16G1227200, MD01G1174400, and MD02G1207200) and hub proteins (PFK, gapN, and HK) were obtained.