CsbZIP1-CsMYB12 mediates the production of bitter-tasting flavonols in tea plants (Camellia sinensis) through a coordinated activator-repressor network

Genome-wide identification and expression analysis of phytochrome-interacting factor genes during abiotic stress responses and secondary metabolism in the tea plant

Phytochrome-interacting factors (PIFs) are pivotal transcriptional regulators controlling photomorphogenesis, environmental responses, and development in plants. However, their specific roles in coordinating adaptation towards abiotic stress and metabolism remain underexplored in tea plants. Here, we identified seven PIF members from four distinct clades (PIF1, PIF3, PIF7, and PIF8). Promoter analysis implicated CsPIFs in integrating light, stress, hormone, and circadian signals. Most CsPIFs exhibited rapid increase in expression under shading, especially CsPIF7b/8a, which displayed significant changes in long-term shading condition. Under drought/salt stress, CsPIF3b emerged as a potential positive regulator. CsPIF3a was induced by low temperature and co-expressed with CsCBF1/3 and CsDREB2A cold response factors. Dual-luciferase assays confirmed that act as negative regulator of the CBF pathway. Expression profiling across 11 tea cultivars associated specific CsPIFs with chlorophyll biosynthesis and accumulation of anthocyanins, flavonols, and other metabolites. In summary, this study highlights the significance of CsPIFs as central coordinators in managing intricate transcriptional reactions to simultaneous abiotic stresses and metabolic adjustments in tea plants. This insight informs future strategies for enhancing this economically crucial crop through crop improvement initiatives.

Differential accumulation patterns of flavor compounds in Longjing 43 and Qunti fresh leaves and during processing responding to altitude changes

Variations in cultivars and cultivation altitudes have significant impacts on tea flavour compounds however lack of comprehensive understanding. This study provided insights into differential accumulation of crucial flavour compounds in response to cultivars, cultivation altitudes, and processing. Twelve flavonoids (262.4 ∼ 275.4 mg•g-1) and 20 amino acids (AAs) (56.5 ∼ 64.8 mg•g-1) were comparative analyzed in 'Longjing 43' and 'Qunti' fresh leaves harvested at low (80 m, LA) and high (500 m, HA) altitudes. Additionally, an in-depth correlation unravelling of 31 alkaloids, 25 fatty acids, 31 saccharides, 8 organic acids, and 7 vitamins and flavonoids/AAs during green tea (GT) and black tea (BT) processing was performed. Enhenced flavonoid accumulation alongside higher AAs and saccharides in HA GT promoted a sweet/mellow flavour. Abundant flavonoids, AAs, and saccharides derivates in LA BT gave rise to a sweet aftertaste. The study presents an integrated illustration of major flavour compounds' differential accumulation patterns and their interrelations, providing new insights into the influence of cultivation conditions on tea flavour.

A functional study reveals CsNAC086 regulated the biosynthesis of flavonols in Camellia sinensis

MAIN CONCLUSION

CsNAC086 was found to promote the expression of CsFLS, thus promoting the accumulation of flavonols in Camellia sinensis. Flavonols, the main flavonoids in tea plants, play an important role in the taste and quality of tea. In this study, a NAC TF gene CsNAC086 was isolated from tea plants and confirmed its regulatory role in the expression of flavonol synthase which is a key gene involved in the biosynthesis of flavonols in tea plant. Yeast transcription-activity assays showed that CsNAC086 has self-activation activity. The transcriptional activator domain of CsNAC086 is located in the non-conserved C-terminal region (positions 171-550), while the conserved NAC domain (positions 1-170) does not have self-activation activity. Silencing the CsNAC086 gene using antisense oligonucleotides significantly decreased the expression of CsFLS. As a result, the concentration of flavonols decreased significantly. In overexpressing CsNAC086 tobacco leaves, the expression of NtFLS was significantly increased. Compared with wild-type tobacco, the flavonols concentration increased. Yeast one-hybrid assays showed CsNAC086 did not directly regulate the gene expression of CsFLS. These findings indicate that CsNAC086 plays a role in regulating flavonols biosynthesis in tea plants, which has important implications for selecting and breeding of high-flavonols-concentration containing tea-plant cultivars.

Transcriptional regulation of flavonol biosynthesis in plants

Flavonols are a class of flavonoids that play a crucial role in regulating plant growth and promoting stress resistance. They are also important dietary components in horticultural crops due to their benefits for human health. In past decades, research on the transcriptional regulation of flavonol biosynthesis in plants has increased rapidly. This review summarizes recent progress in flavonol-specific transcriptional regulation in plants, encompassing characterization of different categories of transcription factors (TFs) and microRNAs as well as elucidation of different transcriptional mechanisms, including direct and cascade transcriptional regulation. Direct transcriptional regulation involves TFs, such as MYB, AP2/ERF, and WRKY, which can directly target the key flavonol synthase gene or other early genes in flavonoid biosynthesis. In addition, different regulation modules in cascade transcriptional regulation involve microRNAs targeting TFs, regulation between activators, interaction between activators and repressors, and degradation of activators or repressors induced by UV-B light or plant hormones. Such sophisticated regulation of the flavonol biosynthetic pathway in response to UV-B radiation or hormones may allow plants to fine-tune flavonol homeostasis, thereby balancing plant growth and stress responses in a timely manner. Based on orchestrated regulation, molecular design strategies will be applied to breed horticultural crops with excellent health-promoting effects and high resistance.

CsMYB73 negatively regulates theanine accumulation mediated by CsGGT2 and CsGGT4 in tea shoots (Camellia sinensis)

Theanine metabolism is a necessary biological process during the planting and production of tea that determines tea quality. There is currently little knowledge about the transcriptional regulation of theanine metabolism in tea plants. In this study, we demonstrated that γ-glutamyl-transpeptidase CsGGT4, as a homologous protein of the theanine hydrolase CsGGT2, exhibited a higher theanine synthesis catalytic efficiency. Homology modeling and molecular docking showed that differential protein structures between CsGGT2 and CsGGT4 implied their different biological functions in tea plants. Theanine content correlated significantly with the expression of CsGGT2, CsGGT4 and the transcription factor CsMYB73 in tea shoots from different seasons. Additionally, CsMYB73 was confirmed to act as a nucleus-localized transcription factor (TF), directly interacts with the CsGGT2 and CsGGT4 promoters, serving as an activator of CsGGT2 and a suppressor of CsGGT4. Consequently, this leads to a negative association with theanine accumulation in tea shoots. Furthermore, the continuous increase in CsMYB73 produced a significantly increase in CsGGT2 expression and inhibited CsGGT4 expression. The present study reveals that the degradation of theanine has been observed to increase, concomitantly with the inhibition of theanine synthesis, resulting in a significant decline in the accumulation of theanine in tea shoots during the process of seasonal greening in 'Huangkui' leaves. This study contributes to the broader comprehension of the intricate transcriptional regulatory hierarchy that governs the metabolism of theanine in tea shoots, offering novel approaches for managing tea plantations and enhancing tea quality.

CsMYB67 participates in the flavonoid biosynthesis of summer tea leaves

Flavonoids are important compounds in tea leaves imparting bitter and astringent taste, which also play key roles in tea plants responding to environmental stress. Our previous study showed that the expression level of CsMYB67 was positively correlated with the accumulation of flavonoids in tea leaves as exposed to sunlight. Here, we newly reported the function of CsMYB67 in regulating flavonoid biosynthesis in tea leaves. CsMYB67 was localized in the nucleus and responded to temperature. The results of transient expression assays showed the co-transformation of CsMYB67 and CsTTG1 promoted the transcription of CsANS promoter in the tobacco system. CsTTG1 was bound to the promoter of CsANS based on the results of yeast one-hybrid (Y1H) and transient expression assays, while CsMYB67 enhanced the transcription of CsANS through protein interaction with CsTTG1 according to the results of yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). Thus, CsMYB67-CsTTG1 module enhanced the anthocyanin biosynthesis through up-regulating the transcription of CsANS. Besides, CsMYB67 also enhanced the transcription of CsFLS and CsUFGT through forming transcription factor complexes. The function of CsMYB67 on flavonoid biosynthesis in tea leaves was validated by gene suppression assay. As CsMYB67 was suppressed, the transcriptional level of CsFLS was greatly reduced, leading to a significant increase in the contents of total catechins and total anthocyanidins. Hence, CsMYB67 plays an important role in regulating the downstream pathway of flavonoid biosynthesis in summer tea leaves.

A cytosine analogue 5-azacitidine improves the accumulation of licochalcone A in licorice Glycyrrhiza inflata

Licochalcone A (LCA) is a characteristic compound of Glycyrrhiza inflata with anti-inflammatory, antioxidant and antitumor activities. However, G. inflata produces LCA in low quantities that does not meet the market demand. In this study, we found that DNA methylation inhibitor 5-azacitidine (5-azaC) successfully improved the LCA contents in G. inflata seedlings. Transcriptome analysis revealed a series of differentially expressed genes (DEGs), including transcription factors such as MYB, ERF, WRKY, and some structural genes related to flavonoid biosynthesis. However, whole genome bisulfite sequencing (BS-seq) results showed little effect of the 5-azaC treatment on the alteration of DNA methylation on these genes, indicating the possibility that 5-azaC acts as a stimulus, but not an epigenetic modulation factor to improve the LCA content in G. inflata. Additionally, we applied the 5-azaC treatment to field plants and hairy roots and successfully increased the LCA contents in both cases. This research demonstrates the feasibility of 5-azaC treatments in future applications to improve plant production of LCA.

An LcMYB111-LcHY5 Module Differentially Activates an LcFLS Promoter in Different Litchi Cultivars

Flavonol synthase (FLS) is the crucial enzyme of the flavonol biosynthetic pathways, and its expression is tightly regulated in plants. In our previous study, two alleles of LcFLS,LcFLS-A and LcFLS-B, have been identified in litchi, with extremely early-maturing (EEM) cultivars only harboring LcFLS-A, while middle-to-late-maturing (MLM) cultivars only harbor LcFLS-B. Here, we overexpressed both LcFLS alleles in tobacco, and transgenic tobacco produced lighter-pink flowers and showed increased flavonol levels while it decreased anthocyanin levels compared to WT. Two allelic promoters of LcFLS were identified, with EEM cultivars only harboring proLcFLS-A, while MLM cultivars only harbor proLcFLS-B. One positive and three negative R2R3-MYB transcription regulators of LcFLS expression were identified, among which only positive regulator LcMYB111 showed a consistent expression pattern with LcFLS, which both have higher expression in EEM than that of MLM cultivars. LcMYB111 were further confirmed to specifically activate proLcFLS-A with MYB-binding element (MBE) while being unable to activate proLcFLS-B with mutated MBE (MBEm). LcHY5 were also identified and can interact with LcMYB111 to promote LcFLS expression. Our study elucidates the function of LcFLS and its differential regulation in different litchi cultivars for the first time.

Uncovering the complex regulatory network of spring bud sprouting in tea plants: insights from metabolic, hormonal, and oxidative stress pathways

The sprouting process of tea buds is an essential determinant of tea quality and taste, thus profoundly impacting the tea industry. Buds spring sprouting is also a crucial biological process adapting to external environment for tea plants and regulated by complex transcriptional and metabolic networks. This study aimed to investigate the molecular basis of bud sprouting in tea plants firstly based on the comparisons of metabolic and transcriptional profiles of buds at different developmental stages. Results notably highlighted several essential processes involved in bud sprouting regulation, including the interaction of plant hormones, glucose metabolism, and reactive oxygen species scavenging. Particularly prior to bud sprouting, the accumulation of soluble sugar reserves and moderate oxidative stress may have served as crucial components facilitating the transition from dormancy to active growth in buds. Following the onset of sprouting, zeatin served as the central component in a multifaceted regulatory mechanism of plant hormones that activates a range of growth-related factors, ultimately leading to the promotion of bud growth. This process was accompanied by significant carbohydrate consumption. Moreover, related key genes and metabolites were further verified during the entire overwintering bud development or sprouting processes. A schematic diagram involving the regulatory mechanism of bud sprouting was ultimately proposed, which provides fundamental insights into the complex interactions involved in tea buds.

CsMYBL2 homologs modulate the light and temperature stress-regulated anthocyanin and catechins biosynthesis in tea plants (Camellia sinensis)

Anthocyanin and catechin production in tea (Camellia sinensis) leaves can positively affect tea quality; however, their regulatory mechanisms are not fully understood. Here we report that, while the CsMYB75- or CsMYB86-directed MYB-bHLH-WD40 (MBW) complexes differentially activate anthocyanin or catechin biosynthesis in tea leaves, respectively, CsMYBL2a and CsMYBL2b homologs negatively modified the light- and temperature-induced anthocyanin and catechin production in both Arabidopsis and tea plants. The MBW complexes activated both anthocyanin synthesis genes and the downstream repressor genes CsMYBL2a and CsMYBL2b. Overexpression of CsMYBL2b, but not CsMYBL2a, repressed Arabidopsis leaf anthocyanin accumulation and seed coat proanthocyanin production. CsMYBL2b strongly and CsMYBL2a weakly repressed the activating effects of CsMYB75/CsMYB86 on CsDFR and CsANS, due to their different EAR and TLLLFR domains and interactions with CsTT8/CsGL3, interfering with the functions of activating MBW complexes. CsMYBL2b and CsMYBL2a in tea leaves play different roles in fine-tuning CsMYB75/CsMYB86-MBW activation of biosynthesis of anthocyanins and catechins, respectively. The CsbZIP1-CsmiR858a-CsMYBL2 module mediated the UV-B- or cold-activated CsMYB75/CsMYB86 regulation of anthocyanin/catechin biosynthesis by repressing CsMYBL2a and CsMYBL2b. Similarly, the CsCOP1-CsbZIP1-CsPIF3 module, and BR signaling as well, mediated the high temperature repression of anthocyanin and catechin biosynthesis through differentially upregulating CsMYBL2b and CsMYBL2a, respectively. The present study provides new insights into the complex regulatory networks in environmental stress-modified flavonoid production in tea plant leaves.

α-Tocopherol application as a countermeasure to UV-B stress in bread wheat (Triticum aestivum L.)

The source of energy for all photoautotrophic organisms is light, which is absorbed by photosynthetic processes and used to transform carbon dioxide and H2O into organic molecules. The majority of UV-B light (280 to 320 nm) is absorbed by stratospheric ozone layer, although some of it does reach at the Earth's surface. Because of the sedentary lifestyle of plants, this form of abiotic stress is unavoidable and can induce growth and even cell death. Ten-day-old calli generated from mature Kirik wheat embryos were subjected to UV-B radiation for 0, 2, 4, and 6 h to examine the function of exogenous α-tocopherol, a lipophilic antioxidant, in wheat tolerance to UV-B radiation stress. The calli were then moved to a callus medium containing α-tocopherol (0, 50, and 100 mg/l) and cultivated there for 20 days after being subjected to UV-B stress. For plant regeneration, embryogenic calli were put on a medium for plant regeneration after 30 days. The findings of this investigation demonstrated that an increase in UV-B exposure period resulted in a substantial drop in the relative growth rate of callus, the rate of embryogenic callus, the rate of responding embryogenic callus, and the number of plants in each explant. On the other hand, with the application of α-tocopherol, all these parameters improved, and the best result was observed in the application of 100 mg/l of α-tocopherol in terms of plant regeneration under UV-B stress.

UV-B promotes flavonoid biosynthesis in Ginkgo biloba by inducing the GbHY5-GbMYB1-GbFLS module

Ginkgo biloba (ginkgo) leaves have medicinal value due to their high levels of secondary metabolites, such as flavonoids. We found that the flavonoid content in ginkgo leaves increases significantly at high altitudes (Qinghai-Tibet Plateau). Considering that high UV-B radiation is among the key environmental characteristics of the Qinghai-Tibet Plateau, we carried out simulated UV-B treatments on ginkgo seedlings and found that the flavonoid content of the leaves increased significantly following the treatments. Combined with results from our previous studies, we determined that the transcription factor GbHY5 may play a key role in responses to UV-B radiation. Overexpression of GbHY5 significantly promoted the accumulation of flavonoids in both ginkgo callus and Arabidopsis thaliana. Furthermore, yeast two-hybrid and real-time quantitative PCR showed that GbHY5 promoted the expression of GbMYB1 by interacting with GbMYB1 protein. Overexpression of GbMYB1 in ginkgo callus and A. thaliana also significantly promoted flavonoid biosynthesis. GbFLS encodes a key enzyme in flavonoid biosynthesis, and its promoter has binding elements of GbHY5 and GbMYB1. A dual-luciferase reporter assay indicated that while GbHY5 and GbMYB1 activated the expression of GbFLS individually, their co-expression achieved greater activation. Our analyses reveal the molecular mechanisms by which the UV-B-induced GbHY5-GbMYB1-GbFLS module promotes flavonoid biosynthesis in ginkgo, and they provide insight into the use of UV-B radiation to enhance the flavonoid content of ginkgo leaves.

Metabolomics provide a novel interpretation of the changes in flavonoids during sea buckthorn (Hippophae rhamnoides L.) drying

Flavonoids are major nutrients in sea buckthorn berries. However, the effects of drying methods on flavonoids in sea buckthorn berries are unclear. In this study, ultra-performance liquid chromatography and metabolomics were adopted to analyse the effects of hot air drying (HAD) and infrared drying (IRD) on flavonoid compounds and antioxidant capacity in sea buckthorn berries. In total, 97 metabolites belonging to 12 classes were identified, including 26 flavones, 23 flavonols, and 11 flavanones. Additionally, 32 differential metabolites were identified among groups. Isorhamnetin and quercetin contents increased in response to HAD and IRD, while (-)-epigallocatechin and (-)-gallocatechin contents decreased. Differential metabolism of flavonoid compounds occurred mainly via the flavonoid biosynthesis and secondary metabolite biosynthesis pathways. Flavonoid compound degradation might be associated with antioxidant activity during drying. This study elucidated the effect of drying on nutritional components of sea buckthorn berries and may guide the improvement of quality during food processing.

Time-series transcriptome provides insights into the gene regulation network involved in the icariin-flavonoid metabolism during the leaf development of Epimedium pubescens

Herba Epimedii (Epimedium) leaves are rich in prenylated flavonol glycosides (PFGs) with high medicinal value. However, the dynamics and regulatory network of PFG biosynthesis remain largely unclear. Here, we combined metabolite profiling (targeted to PFGs) and a high-temporal-resolution transcriptome to elucidate PFGs' regulatory network in Epimedium pubescens and identified key candidate structural genes and transcription factors (TFs) involved in PFG accumulation. Chemical profile analysis revealed that PFG content was quite different between buds and leaves and displayed a continuous decline with leaf development. The structural genes are the determinant reasons, and they are strictly regulated by TFs under temporal cues. We further constructed seven time-ordered gene co-expression networks (TO-GCNs) of PFG biosynthesis genes (including EpPAL2, EpC4H, EpCHS2, EpCHI2, EpF3H, EpFLS3, and EpPT8), and three flavonol biosynthesis routines were then predicted. The TFs involved in TO-GCNs were further confirmed by WGCNA analysis. Fourteen hub genes, comprising 5 MYBs, 1 bHLH, 1 WD40, 2 bZIPs, 1 BES1, 1 C2H2, 1 Trihelix, 1 HD-ZIP, and 1 GATA were identified as candidate key TFs. The results were further validated by TF binding site (TFBS) analysis and qRT-PCR. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of PFGs biosynthesis, enriching the gene resources, which will guide further research on PFG accumulation in Epimedium.

The CmMYB3 transcription factors isolated from the Chrysanthemum morifolium regulate flavonol biosynthesis in Arabidopsis thaliana

Chrysanthemum morifolium MYB3 factors are transcriptional activators for the regulation of flavonol biosynthesis. Flavonol was not only the critical secondary metabolite participating in the growth and development of plants but also the main active ingredient in medicinal chrysanthemum. However, few pieces of research revealed the transcriptional regulation of flavonol biosynthesis in Chrysanthemum morifolium. Here, we isolated two CmMYB3 transcription factors (CmMYB3a and CmMYB3b) from the capitulum of Chrysanthemum morifolium cv 'Hangju'. According to the sequence characteristics, the CmMYB3a and CmMYB3b belonged to the R2R3-MYB subgroup 7, whose members were often reported to regulate flavonol biosynthesis positively. CmMYB3a and CmMYB3b factors were identified to localize in the nucleus by subcellular localization assay. Besides, both of them have obvious transcriptional self-activation activity in their C-terminal. After the overexpression of CmMYB3 genes in Nicotiana benthamiana and Arabidopsis thaliana, the flavonol contents in plants were increased, and the expression of AtCHS, AtCHI, AtF3H, and AtFLS genes in A. thaliana was also improved. Interestingly, the CmMYB3a factor had stronger functions in improving flavonol contents and related gene expression levels than CmMYB3b. The interaction analysis between transcription factors and promoters suggested that CmMYB3 could bind and activate the promoters of CmCHI and CmFLS genes in C. morifolium, and CmMYB3a also functioned more powerfully. Overall, these results indicated that CmMYB3a and CmMYB3b work as transcriptional activators in controlling flavonol biosynthesis.

Transcriptional Analysis of Tea Plants (Camellia sinensis) in Response to Salicylic Acid Treatment

Salicylic acid (SA) is an important plant hormone and signal required for establishing resistance to diverse pathogens and plant diseases. The abundant polyphenols in tea plants also defend plants from biotic and abiotic stresses. However, whether exogenous SA would increase the resistance of tea plants to adversity and the relationship between SA and polyphenols are still poorly understood. Here, we carried out SA treatment on tea seedlings and performed transcriptome sequencing. SA treatment inhibited the phenylpropanoid and flavonoid metabolic pathways but promoted the lignin metabolic pathways. The increased accumulation of lignin in tea leaves after treating with SA indicated that lignin might coordinate SA, enhance, and improve plant defense and disease resistance. Simultaneously, an SA-inducible flavonoid glucosyltransferase (CsUGT0554) specifically involved in 7-OH site glycosylation was characterized in vitro. These results provided valuable information about the effects of SA on tea seedlings and the molecular basis for SA-mediated immune responses.

High Light Intensity Triggered Abscisic Acid Biosynthesis Mediates Anthocyanin Accumulation in Young Leaves of Tea Plant (Camellia sinensis)

There is increasing interest in the production and consumption of tea (Camellia sinensis L.) processed from purple-leaved cultivar due to their high anthocyanin content and health benefits. However, how and why seasonal changes affect anthocyanin accumulation in young tea leaves still remains obscured. In this study, anthocyanin and abscisic acid (ABA) contents in young leaves of Zifuxing 1 (ZFX1), a cultivar with new shoots turning to purple in Wuyi Mountain, a key tea production region in China, were monitored over four seasons. Young leaves produced in September were highly purplish, which was accompanied with higher anthocyanin and ABA contents. Among the environmental factors, the light intensity in particular was closely correlated with anthocyanin and ABA contents. A shade experiment also indicated that anthocyanin content significantly decreased after 168 h growth under 75% shade, but ABA treatment under the shade conditions sustained anthocyanin content. To confirm the involvement of ABA in the modulation of anthocyanin accumulation, anthocyanin, carotenoids, chlorophyll, ABA, jasmonic acid (JA), and salicylic acid (SA) in the young leaves of four cultivars, including ZFX1, Zijuan (ZJ), wherein leaves are completely purple, Rougui (RG) and Fudingdabaicha (FDDB) wherein leaves are green, were analyzed, and antioxidant activities of the leaf extracts were tested. Results showed that ABA, not other tested hormones, was significantly correlated with anthocyanin accumulation in the purple-leaved cultivars. Cultivars with higher anthocyanin contents exhibited higher antioxidant activities. Subsequently, ZFX1 plants were grown under full sun and treated with ABA and fluridone (Flu), an ABA inhibitor. ABA treatment elevated anthocyanin level but decreased chlorophyll contents. The reverse was true to those treated with Flu. To pursue a better understanding of ABA involvement in anthocyanin accumulation, RNA-Seq was used to analyze transcript differences among ABA- or Flu-treated and untreated ZFX1 plants. Results indicated that the differentially expressed genes in ABA or Flu treatment were mainly ABA signal sensing and metabolism-related genes, anthocyanin accumulation-related genes, light-responsive genes, and key regulatory MYB transcription factors. Taking all the results into account, a model for anthocyanin accumulation in ZFX1 cultivar was proposed: high light intensity caused reactive oxygen stress, which triggered the biosynthesis of ABA; ABA interactions with transcription factors, such as MYB-enhanced anthocyanin biosynthesis limited chlorophyll and carotenoid accumulation; and transport of anthocyanin to vacuoles resulting in the young leaves of ZFX1 with purplish coloration. Further research is warranted to test this model.

Variations of stomata development in tea plant (Camellia sinensis) leaves in different light and temperature environments and genetic backgrounds

Stomata perform important functions in plant photosynthesis, respiration, gas exchange, and interactions with environments. However, tea plant stomata development and functions are not known. Here, we show morphological changes during stomata development and genetic dissection of stomata lineage genes regulating stomata formation in tea developing leaves. Different tea plant cultivars displayed clear variations in the stomata development rate, density and size, which are closely related to their tolerance against dehydration capabilities. Whole sets of stomata lineage genes were identified to display predicted functions in regulating stomatal development and formation. The stomata development and lineage genes were tightly regulated by light intensities and high or low temperature stresses, which affected stomata density and function. Furthermore, lower stomatal density and larger size were observed in triploid tea varieties as compared to those in diploid plant. Key stomata lineage genes such as CsSPCHs, CsSCRM, and CsFAMA showed much lower expression levels, whereas negative regulators CsEPF1 and CsYODAs had higher expression levels in triploid than in diploid tea varieties. Our study provides new insight into tea plant stomatal morphological development and the genetic regulatory mechanisms on stomata development under abiotic stresses and genetic backgrounds. The study lays a foundation for future exploring of the genetic improvement of water use efficiency in tea plants for living up to the challenge of global climate change.

A glutathione S-transferase GhTT19 determines flower petal pigmentation via regulating anthocyanin accumulation in cotton

Anthocyanin accumulations in the flowers can improve seed production of hybrid lines, and produce higher commodity value in cotton fibre. However, the genetic mechanism underlying the anthocyanin pigmentation in cotton petals is poorly understood. Here, we showed that the red petal phenotype was introgressed from Gossypium bickii through recombination with the segment containing the R₃ ^bic region in the A07 chromosome of Gossypium hirsutum variety LR compared with the near-isogenic line of LW with white flower petals. The cyanidin-3-O-glucoside (Cy3G) was the major anthocyanin in red petals of cotton. A GhTT19 encoding a TT19-like GST was mapped to the R₃ ^bic site associated with red petals via map-based cloning, but GhTT19 homologue gene from the D genome was not expressed in G. hirsutum. Intriguingly, allelic variations in the promoters between GhTT19^LW and GhTT19^LR , rather than genic regions, were found as genetic causal of petal colour variations. GhTT19-GFP was found localized in both the endoplasmic reticulum and tonoplast for facilitating anthocyanin transport. An additional MYB binding element found only in the promoter of GhTT19^LR , but not in that of GhTT19^LW , enhanced its transactivation by the MYB activator GhPAP1. The transgenic analysis confirmed the function of GhTT19 in regulating the red flower phenotype in cotton. The essential light signalling component GhHY5 bonded to and activated the promoter of GhPAP1, and the GhHY5-GhPAP1 module together regulated GhTT19 expression to mediate the light-activation of petal anthocyanin pigmentation in cotton. This study provides new insights into the molecular mechanisms for anthocyanin accumulation and may lay a foundation for faster genetic improvement of cotton.

Evolutionary Landscape of Tea Circular RNAs and Its Contribution to Chilling Tolerance of Tea Plant

Chilling stress threatens the yield and distribution pattern of global crops, including the tea plant (Camellia sinensis), one of the most important cash crops around the world. Circular RNA (circRNA) plays roles in regulating plant growth and biotic/abiotic stress responses. Understanding the evolutionary characteristics of circRNA and its feedbacks to chilling stress in the tea plant will help to elucidate the vital roles of circRNAs. In the current report, we systematically identified 2702 high-confidence circRNAs under chilling stress in the tea plant, and interestingly found that the generation of tea plant circRNAs was associated with the length of their flanking introns. Repetitive sequences annotation and DNA methylation analysis revealed that the longer flanking introns of circRNAs present more repetitive sequences and higher methylation levels, which suggested that repeat-elements-mediated DNA methylation might promote the circRNAs biogenesis in the tea plant. We further detected 250 differentially expressed circRNAs under chilling stress, which were functionally enriched in GO terms related to cold/stress responses. Constructing a circRNA-miRNA-mRNA interaction network discovered 139 differentially expressed circRNAs harboring potential miRNA binding sites, which further identified 14 circRNAs that might contribute to tea plant chilling responses. We further characterized a key circRNA, CSS-circFAB1, which was significantly induced under chilling stress. FISH and silencing experiments revealed that CSS-circFAB1 was potentially involved in chilling tolerance of the tea plant. Our study emphasizes the importance of circRNA and its preliminary role against low-temperature stress, providing new insights for tea plant cold tolerance breeding.

Effects of Preharvest Shading on Dynamic Changes in Metabolites, Gene Expression, and Enzyme Activity of Three Tea Types during Processing

Preharvest shading significantly influences tea flavor. However, little attention has been given to the mechanism of shading on metabolites, genes, and enzymes in the processing of different tea types. Our study identified 1028 nonvolatile metabolites covering 10 subclasses using a widely targeted metabolome. The results show that shading had a greater effect on the compositions of amino acids, flavonoids, and theaflavins in tea leaves. The combined transcriptomics and enzyme activity analysis results indicate that the upregulated expression of asparagine, aspartate, and tryptophan synthesis genes and proteolytic enzymes promoted the accumulation of amino acids. The downregulated enzyme genes resulted in the reduction of nongalloylated catechins and flavonoid glycosides. Simultaneously, the accumulation of TFs in shaded tea was due to the enhanced enzymatic activities of polyphenol oxidase and peroxidase during processing. Theaflavin-3-3'-di-O-gallate was also significantly positively correlated with the antioxidant and hypoglycemic activities of shaded tea. The results contribute to a better understanding of how preharvest treatments influence summer tea quality.

Malate-mediated CqMADS68 enhances aluminum tolerance in quinoa seedlings through interaction with CqSTOP6, CqALMT6 and CqWRKY88

Aluminum (Al) stress in acidic soils has severe negative effects on crop productivity. In this study, the alleviating effect and related mechanism of malate on Al stress in quinoa (Chenopodium quinoa) seedlings were investigated. The findings indicated that malate alleviated the growth inhibition of quinoa seedlings under Al stress, maintained the enzymatic and nonenzymatic antioxidant systems, and aided resistance to the damage caused by excessive reactive oxygen species (ROS). Under Al stress, malate significantly increased the contents of chlorophyll and carotenoids in quinoa shoots by 103.8% and 240.7%, and significantly increased the ratios of glutathione (GSH)/oxidized glutathione (GSSG), and ascorbate (AsA)/dehydroascorbate (DHA) in roots by 59.9% and 699.2%, respectively. However, malate significantly decreased the superoxide radical (O₂•^-), hydrogen peroxide (H₂O₂), malondialdehyde (MDA) and Al contents in quinoa roots under Al stress by 32.7%, 60.9%, 63.1% and 49%, respectively. Moreover, the CqMADS family and the Al stress-responsive gene families (CqSTOP, CqALMT, and CqWRKY) were identified from the quinoa genome. Comprehensive expression profiling identified CqMADS68 as being involved in malate-mediated Al resistance. Transient overexpression of CqMADS68 increased Al tolerance in quinoa seedlings. More importantly, we found that CqMADS68 regulated the expression of CqSTOP6, CqALMT6 and CqWRKY88 and further demonstrated the interaction of CqMADS68 with CqSTOP6, CqALMT6 and CqWRKY88 by bimolecular fluorescence complementation (BIFC) experiments. Moreover, transient overexpression and physiological and biochemical analyses demonstrated that CqSTOP6, CqALMT6 and CqWRKY88 could also improve Al tolerance by maintaining the antioxidant capacity of quinoa seedlings. Taken together, these findings reveal that CqMADS68, CqSTOP6, CqALMT6 and CqWRKY88 may be important contributors to the Al tolerance regulatory network in quinoa, providing new insights into Al stress resistance.

Integrating metabolite and transcriptome analysis revealed the different mechanisms of characteristic compound biosynthesis and transcriptional regulation in tea flowers

The flowers of tea plants (Camellia sinensis), as well as tea leaves, contain abundant secondary metabolites and are big potential resources for the extraction of bioactive compounds or preparation of functional foods. However, little is known about the biosynthesis and transcriptional regulation mechanisms of those metabolites in tea flowers, such as terpenoid, flavonol, catechins, caffeine, and theanine. This study finely integrated target and nontarget metabolism analyses to explore the metabolic feature of developing tea flowers. Tea flowers accumulated more abundant terpenoid compounds than young leaves. The transcriptome data of developing flowers and leaves showed that a higher expression level of later genes of terpenoid biosynthesis pathway, such as Terpene synthases gene family, in tea flowers was the candidate reason of the more abundant terpenoid compounds than in tea leaves. Differently, even though flavonol and catechin profiling between tea flowers and leaves was similar, the gene family members of flavonoid biosynthesis were selectively expressed by tea flowers and tea leaves. Transcriptome and phylogenetic analyses indicated that the regulatory mechanism of flavonol biosynthesis was perhaps different between tea flowers and leaves. However, the regulatory mechanism of catechin biosynthesis was perhaps similar between tea flowers and leaves. This study not only provides a global vision of metabolism and transcriptome in tea flowers but also uncovered the different mechanisms of biosynthesis and transcriptional regulation of those important compounds.

Integrated metabolic, transcriptomic and chromatin accessibility analyses provide novel insights into the competition for anthocyanins and flavonols biosynthesis during fruit ripening in red apple

Fruit ripening is accompanied by a wide range of metabolites and global changes in gene expression that are regulated by various factors. In this study, we investigated the molecular differences in red apple 'Hongmantang' fruits at three ripening stages (PS1, PS5 and PS9) through a comprehensive analysis of metabolome, transcriptome and chromatin accessibility. Totally, we identified 341 and 195 differentially accumulated metabolites (DAMs) in comparison I (PS5_vs_PS1) and comparison II (PS9_vs_PS5), including 57 and 23 differentially accumulated flavonoids (DAFs), respectively. Intriguingly, among these DAFs, anthocyanins and flavonols showed opposite patterns of variation, suggesting a possible competition between their biosynthesis. To unveil the underlying mechanisms, RNA-Seq and ATAC-Seq analyses were performed. A total of 852 DEGs significantly enriched in anthocyanin metabolism and 128 differential accessible regions (DARs) significantly enriched by MYB-related motifs were identified as up-regulated in Comparison I but down-regulated in Comparison II. Meanwhile, the 843 DEGs significantly enriched in phenylalanine metabolism and the 364 DARs significantly enriched by bZIP-related motifs showed opposite trends. In addition, four bZIPs and 14 MYBs were identified as possible hub genes regulating the biosynthesis of flavonols and anthocyanins. Our study will contribute to the understanding of anthocyanins and flavonols biosynthesis competition in red apple fruits during ripening.

Biosynthesis, distribution, nutritional and organoleptic properties of bitter compounds in fruit and vegetables

Compounds that confer a bitter taste on fruits and vegetables (FAVs) play crucial roles in both plant defense and health promotion. This review details the current knowledge of the distribution, properties (toxicity, pharmacological effects and receptors) and environmental plant responses relating to the biosynthesis, catabolism and transcriptional regulation of 53 bitter plant metabolites in diverse species of FAVs. Some bitter compounds, such as flavonoids, are common in all plant species and make a minor contribution to bitter flavor, but many are synthesized only in specific taxa. They make major contributions to the bitter taste of the corresponding species and some also have significant pharmacological effects. Levels of bitter metabolites are genetically determined, but various environmental cues can affect their final concentration during preharvest development and postharvest storage processes. Molecular approaches are helping to unravel the mechanisms of biosynthesis and regulation of bitter compounds in diverse crop species. This review not only discusses the theoretical basis for utilizing breeding programs and other agricultural technologies to produce FAVs with improved safety, favorable taste and healthier profiles, but also suggests new directions for the utilization of bitter compounds in FAVs for the development of natural pesticides and health-promoting medicines.

Unravelling the consecutive glycosylation and methylation of flavonols in peach in response to UV-B irradiation

Flavonol glycosides are bioactive compounds important for plant defence and human nutrition. Glycosylation and methylation play an important role in enriching the diversity of flavonols in response to the environment. Peach flowers and fruit are rich in flavonol diglycosides such as isorhamnetin 3-O-rutinoside (I3Rut), kaempferol 3-O-rutinoside and quercetin 3-O-rutinoside, and flavonol monoglycosides such as I 3-O-glucoside and Q 3-O-galactoside. UV-B irradiation of fruit significantly induced accumulation of all these flavonol glycosides. Candidate biosynthetic genes induced by UV-B were identified by genome homology searches and the in vitro catalytic activities of purified recombinant proteins determined. PpUGT78T3 and PpUGT78A2 were identified as flavonol 3-O-glucosyltransferase and 3-O-galactosyltransferase, respectively. PpUGT91AK6 was identified as flavonol 1,6-rhamnosyl trasferase catalysing the formation of flavonol rutinosides and PpFOMT1 was identified as a flavonol O-methyltransferase that methylated Q at the 3'-OH-OH to form isorhamnetin derivatives. Transient expression in Nicotiana benthamiana confirmed the specificity of PpUGT78T3 as a flavonol 3-O-glucosyltransferase, PpUGT78A2 as a 3-O-galactosyltransferase, PpUGT91AK6 as a 1,6-rhamnosyltrasferase and PpFOMT1 as an O-methyltransferase. This study provides new insights into the mechanisms of glycosylation and methylation of flavonols, especially the formation of flavonol diglycosides such as I3Rut, and will also be useful for future potential metabolic engineering of complex flavonols.

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.

Diverse roles of MYB transcription factors in regulating secondary metabolite biosynthesis, shoot development, and stress responses in tea plants (Camellia sinensis)

Tea (Camellia sinensis) is concocted from tea plant shoot tips that produce catechins, caffeine, theanine, and terpenoids, which collectively determine the rich flavors and health benefits of the infusion. However, little is known about the integrated regulation of shoot tip development and characteristic secondary metabolite biosynthesis in tea plants. Here, we demonstrate that MYB transcription factors (TFs) play key and yet diverse roles in regulating leaf and stem development, secondary metabolite biosynthesis, and environmental stress responses in tea plants. By integrating transcriptomic and metabolic profiling data in different tissues at a series of developmental stages or under various stress conditions, alongside biochemical and genetic analyses, we predicted the MYB TFs involved in regulating shoot development (CsMYB2, 98, 107, and 221), epidermal cell initiation (CsMYB184, 41, 139, and 219), stomatal initiation (CsMYB113 and 153), and the biosynthesis of flavonoids (including catechins, anthocyanins, and flavonols; CsMYB8 and 99), caffeine (CsMYB85 and 86), theanine (CsMYB9 and 49), carotenoids (CsMYB110), mono-/sesquiterpenoid volatiles (CsMYB68, 147, 148, and 193), lignin (CsMYB164 and 192), and indolic compounds (CsMYB139, 162, and 198), as well as the MYB TFs that are likely involved in hormone signaling-mediated environmental stress and defense responses. We characterized the functions of some key MYBs in regulating flavonoid and carotenoid biosynthesis for tea quality and flavor. This study provides a cross-family analysis of MYBs in tea alongside new insights into the coordinated regulation of tea plant shoot development and secondary metabolism, paving the way towards understanding of tea quality trait formation and genetic improvement of quality tea plants.

Integrative Analysis of Long- and Short-Read Transcriptomes Identify the Regulation of Terpenoids Biosynthesis Under Shading Cultivation in Oenanthe javanica

Water dropwort (Oenanthe javanica) is a popular vegetable with high nutritional value and distinctive flavor. The flavor is mainly correlate with the biosynthesis of terpenoids. Shading cultivation was used to improve the flavor in the production of water dropwort. However, the changes of terpenoids and the genes involved in terpenoids biosynthesis under shading treatment remains unclear. In this study, the long- and short-reads transcriptomes of water dropwort were constructed. In total, 57,743 non-redundant high-quality transcripts were obtained from the transcriptome. 28,514 SSRs were identified from non-redundant transcripts and the mono-nucleotide repeats were the most abundant SSRs. The lncRNAs of water dropwort were recognized and their target genes were predicted. The volatile compound contents in petioles and leaf blades of water dropwort were decreased after the shading treatment. The DEGs analysis was performed to identify the terpenoids biosynthesis genes. The results indicated that 5,288 DEGs were differentially expressed in petiole, of which 22 DEGs were enriched in the terpenoids backbone biosynthesis pathway. A total of 12 DEGs in terpenoids biosynthesis pathway were selected and further verified by qRT-PCR assay, demonstrating that the terpenoids biosynthesis genes were down-regulated under shading treatment. Here, the full-length transcriptome was constructed and the regulatory genes related to terpenoids biosynthesis in water dropwort were also investigated. These results will provide useful information for future researches on functional genomics and terpenoids biosynthesis mechanism in water dropwort.

Carbon and Nitrogen Metabolism Are Jointly Regulated During Shading in Roots and Leaves of Camellia Sinensis

Numerous studies have shown that plant shading can promote the quality of green tea. However, the association of shading with metabolic regulation in tea leaves and roots remains unelucidated. Here, the metabolic profiling of two tea cultivars ("Xiangfeicui" and "Jinxuan") in response to shading and relighting periods during the summer season was performed using non-targeted metabolomics methods. The metabolic pathway analyses revealed that long-term shading remarkably inhibit the sugar metabolism such as glycolysis, galactose metabolism, and pentose phosphate pathway in the leaves and roots of "Xiangfeicui," and "Jinxuan" were more sensitive to light recovery changes. The lipid metabolism in the leaves and roots of "Xiangfeicui" was promoted by short-term shading, while it was inhibited by long-term shading. In addition, the intensity of the flavonoid metabolites in the leaves and roots of "Jinxuan" were upregulated with a trend of rising first and then decreasing under shading, and five flavonoid synthesis genes showed the same trend (F3H, F3'5'H, DFR, ANS, and ANR). Simultaneously, the amino acids of the nitrogen metabolism in the leaves and roots of the two cultivars were significantly promoted by long-term shading, while the purine and caffeine metabolism was inhibited in the leaves of "Xiangfeicui." Interestingly, CsGS1.1 and CsTSI, amino acid synthase genes was upregulated in the leaves and roots of two cultivars. These results indicated that shading could participate in carbon and nitrogen metabolic regulation of both leaf and root, and root metabolism could have a positive association with leaf metabolism to promote the shaded tea quality.

Genome-Wide Identification of the PMEI Gene Family in Tea Plant and Functional Analysis of CsPMEI2 and CsPMEI4 Through Ectopic Overexpression

Pectin methylesterase inhibitor (PMEI) inhibits pectin methylesterase (PME) activity at post-translation level, which plays core roles in vegetative and reproductive processes and various stress responses of plants. However, the roles of PMEIs in tea plant are still undiscovered. Herein, a total of 51 CsPMEIs genes were identified from tea plant genome. CsPMEI1-4 transcripts were varied in different tea plant tissues and regulated by various treatments, including biotic and abiotic stresses, sugar treatments, cold acclimation and bud dormancy. Overexpression of CsPMEI4 slightly decreased cold tolerance of transgenic Arabidopsis associated with lower electrolyte leakage, soluble sugars contents and transcripts of many cold-induced genes as compared to wild type plants. Under long-day and short-day conditions, CsPMEI2/4 promoted early flowering phenotypes in transgenic Arabidopsis along with higher expression levels of many flowering-related genes. Moreover, overexpression of CsPMEI2/4 decreased PME activity, but increased sugars contents (sucrose, glucose, and fructose) in transgenic Arabidopsis as compared with wild type plants under short-day condition. These results indicate that CsPMEIs are widely involved in tea plant vegetative and reproductive processes, and also in various stress responses. Moreover, CsPMEI4 negatively regulated cold response, meanwhile, CsPMEI2/4 promoted early flowering of transgenic Arabidopsis via the autonomous pathway. Collectively, these results open new perspectives on the roles of PMEIs in tea plant.

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.

Mechanism Underlying the Shading-Induced Chlorophyll Accumulation in Tea Leaves

Besides aroma and taste, the color of dry tea leaves, tea infusion, and infused tea leaves is also an important index for tea quality. Shading can significantly increase the chlorophyll content of tea leaves, leading to enhanced tea leaf coloration. However, the underlying regulatory mechanism remains unclear. In this study, we revealed that the expressions of chlorophyll synthesis genes were significantly induced by shading, specially, the gene encoding protochlorophyllide oxidoreductase (CsPOR). Indoor control experiment showed that decreased light intensity could significantly induce the expression of CsPOR, and thus cause the increase of chlorophyll content. Subsequently, we explored the light signaling pathway transcription factors regulating chlorophyll synthesis, including CsPIFs and CsHY5. Through expression level and subcellular localization analysis, we found that CsPIF3-2, CsPIF7-1, and CsHY5 may be candidate transcriptional regulators. Transcriptional activation experiments proved that CsHY5 inhibits CsPORL-2 transcription. In summary, we concluded that shading might promote the expression of CsPORL-2 by inhibiting the expression of CsHY5, leading to high accumulation of chlorophyll in tea leaves. The results of this study provide insights into the mechanism regulating the improvements to tea plant quality caused by shading.

Screening the Key Region of Sunlight Regulating the Flavonoid Profiles of Young Shoots in Tea Plants (Camellia sinensis L.) Based on a Field Experiment

Both UV and blue light have been reported to regulate the biosynthesis of flavonoids in tea plants; however, the respective contributions of the corresponding regions of sunlight are unclear. Additionally, different tea cultivars may respond differently to altered light conditions. We investigated the responses of different cultivars (‘Longjing 43’, ‘Zhongming 192’, ‘Wanghai 1’, ‘Jingning 1’ and ‘Zhonghuang 2’) to the shade treatments (black and colored nets) regarding the biosynthesis of flavonoids. For all cultivars, flavonol glycosides showed higher sensitivity to light conditions compared with catechins. The levels of total flavonol glycosides in the young shoots of different tea cultivars decreased with the shade percentages of polyethylene nets increasing from 70% to 95%. Myricetin glycosides and quercetin glycosides were more sensitive to light conditions than kaempferol glycosides. The principal component analysis (PCA) result indicated that shade treatment greatly impacted the profiles of flavonoids in different tea samples based on the cultivar characteristics. UV is the crucial region of sunlight enhancing flavonol glycoside biosynthesis in tea shoots, which is also slight impacted by light quality according to the results of the weighted correlation network analysis (WGCNA). This study clarified the contributions of different wavelength regions of sunlight in a field experiment, providing a potential direction for slightly bitter and astringent tea cultivar breeding and instructive guidance for practical field production of premium teas based on light regimes.

The Flavonoid Biosynthesis Network in Plants

Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses.