The light-induced transcription factor FtMYB116 promotes accumulation of rutin in Fagopyrum tataricum

Enhancing secondary metabolite biosynthesis from ethnomedicinal plant Solanum nigrum L. through cytogenetically stable mass propagation, transgenic hairy root induction, and using different LED light and culture vessels for hairy root culture

This study aimed for stepwise enhancement of bioactive compound production in ethnomedicinal plant Solanum nigrum through novel approaches of micropropagation, hairy root induction, and treatment of hairy roots with various physical conditions. Polyamines were first-time used for in vitro shoot multiplication of S. nigrum, where highest shoot numbers (55.70 ± 0.64) were observed in Murashige and Skoog's (MS) medium with 0.2 mg/L thiadiazuron + 20 mg/L spermine, whereas maximum root numbers (34.20 ± 0.80) were observed in ½MS medium with 0.5 mg/L indole-3-acetic acid. Pioneer studies of cytogenetical fidelity assessment through inter simple sequence repeat (ISSR) and start codon targeted (SCoT) markers, and chromosome analysis approved genetic uniformity in regenerated plants. Cent percent hairy roots were induced from in vitro S. nigrum leaves (25-30 roots/explant) using Agrobacterium rhizogenes (A4 strain). PCR of transgenes confirmed the transformed nature and absence of bacterial contamination in hairy roots. HPLC studies indicated greater secondary metabolites in hairy roots than in vivo and in vitro plants. Hairy root culture with different culture vessels revealed overall better biomass gain in tightly sealed vessels. However, hairy root cultures treated with red light showed highest biomass accumulation in fresh (2380.13 ± 16.83 mg) and dry (174.66 ± 4.68 mg) weight with maximum solasodine (3.25 ± 0.04 mg/g) and diosgenin (1.03 ± 0.02 mg/g) contents, whereas optimal production of caffeic (3.51 ± 0.05 mg/g), coumaric (2.53 ± 0.06 mg/g), ellagic (0.18 ± 0.02 mg/g), and ferulic (2.17 ± 0.03 mg/g) acid production was found in blue light. These reproducible protocols can be utilized in future bioreactor-mediated mass-culture of hairy roots for commercial-level secondary metabolite production from S. nigrum.

The Seed-Specific Rutin-Degrading Enzyme FtBGLU29 is a Key Factor Promoting the Accumulation of the Bitter Compound Quercetin in Tartary Buckwheat

Rutin-degrading enzymes play a crucial role in catalyzing the hydrolysis of rutin (quercetin 3-O-rutinoside) into the bitter compound quercetin, contributing significantly to the bitterness of Tartary buckwheat (Fagopyrum tataricum) (TB). Mitigating this bitterness is vital for improving the palatability and marketability of TB products. In this study, we integrated genomic and transcriptomic data with molecular docking analyses to identify 12 potential rutin-degrading enzymes in TB. Among them, FtBGLU29 exhibited a stable binding affinity for rutin and significantly higher expression levels, specifically in TB seeds. This unique expression was confirmed through Native-PAGE and MALDI-TOF/TOF-MS, which identified FtBGLU29 as the predominant rutin-degrading enzyme in TB seeds. In vitro hydrolysis experiments revealed that FtBGLU29 efficiently catalyzes the conversion of rutin to quercetin upon the hydration of TB flour. Functional studies showed that FtBGLU29 overexpression in TB seeds significantly enhanced the rutin hydrolysis rate relative to the control group (p < 0.05). In conclusion, this study establishes FtBGLU29 as a key enzyme in the degradation of rutin in TB seeds, highlighting its critical role in enhancing the enzymatic conversion efficiency and potentially reducing the bitterness of TB products.

Effects of Different LED Spectra on the Antioxidant Capacity and Nitrogen Metabolism of Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)

Light quality optimization is a cost-effective method for increasing leafy vegetable quality in plant factories. Light-emitting diodes (LEDs) that enable the precise modulation of light quality were used in this study to examine the effects of red-blue (RB), red-blue-green (RBG), red-blue-purple (RBP), and red-blue-far-red (RBF) lights on the growth, antioxidant capacity, and nitrogen metabolism of Chinese cabbage leaves, while white light served as the control (CK). Results showed that the chlorophyll, carotenoid, vitamin C, amino acid, total flavonoid, and antioxidant levels of Chinese cabbage were all significantly increased under RBP combined light treatment. Meanwhile, RBG combined light treatment significantly increased the levels of amino acids but decreased the nitrite content of Chinese cabbage. In addition, RBF combined light treatment remarkably increased the amino acid levels but decreased the antioxidant capacity of Chinese cabbage. In conclusion, the addition of purple light to red-blue light was effective in improving the nutritional value and antioxidant capacity of Chinese cabbage. This light condition can be used as a model for a supplemental lighting strategy for leafy vegetables in plant factory production.

FtMYB163 Gene Encodes SG7 R2R3-MYB Transcription Factor from Tartary Buckwheat (Fagopyrum tataricum Gaertn.) to Promote Flavonol Accumulation in Transgenic Arabidopsis thaliana

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a coarse grain crop rich in flavonoids that are beneficial to human health because they function as anti-inflammatories and provide protection against cardiovascular disease and diabetes. Flavonoid biosynthesis is a complex process, and relatively little is known about the regulatory pathways involved in Tartary buckwheat. Here, we cloned and characterized the FtMYB163 gene from Tartary buckwheat, which encodes a member of the R2R3-MYB transcription factor family. Amino acid sequence and phylogenetic analysis indicate that FtMYB163 is a member of subgroup 7 (SG7) and closely related to FeMYBF1, which regulates flavonol synthesis in common buckwheat (F. esculentum). We demonstrated that FtMYB163 localizes to the nucleus and has transcriptional activity. Expression levels of FtMYB163 in the roots, stems, leaves, flowers, and seeds of F. tataricum were positively correlated with the total flavonoid contents of these tissues. Overexpression of FtMYB163 in transgenic Arabidopsis enhanced the expression of several genes involved in early flavonoid biosynthesis (AtCHS, AtCHI, AtF3H, and AtFLS) and significantly increased the accumulation of several flavonoids, including naringenin chalcone, naringenin-7-O-glucoside, eriodictyol, and eight flavonol compounds. Our findings demonstrate that FtMYB163 positively regulates flavonol biosynthesis by changing the expression of several key genes in flavonoid biosynthetic pathways.

Buckwheat OMICS: present status and future prospects

Buckwheat (Fagopyrum spp.) is an underutilized resilient crop of North Western Himalayas belonging to the family Polygonaceae and is a source of essential nutrients and therapeutics. Common Buckwheat and Tatary Buckwheat are the two main cultivated species used as food. It is the only grain crop possessing rutin, an important metabolite with high nutraceutical potential. Due to its inherent tolerance to various biotic and abiotic stresses and a short life cycle, Buckwheat has been proposed as a model crop plant. Nutritional security is one of the major concerns, breeding for a nutrient-dense crop such as Buckwheat will provide a sustainable solution. Efforts toward improving Buckwheat for nutrition and yield are limited due to the lack of available: genetic resources, genomics, transcriptomics and metabolomics. In order to harness the agricultural importance of Buckwheat, an integrated breeding and OMICS platforms needs to be established that can pave the way for a better understanding of crop biology and developing commercial varieties. This, coupled with the availability of the genome sequences of both Buckwheat species in the public domain, should facilitate the identification of alleles/QTLs and candidate genes. There is a need to further our understanding of the molecular basis of the genetic regulation that controls various economically important traits. The present review focuses on: the food and nutritional importance of Buckwheat, its various omics resources, utilization of omics approaches in understanding Buckwheat biology and, finally, how an integrated platform of breeding and omics will help in developing commercially high yielding nutrient rich cultivars in Buckwheat.

Regulatory Module FtMYB5/6-FtGBF1-FtUFGT163 Promotes Rutin Biosynthesis in Tartary Buckwheat

Tartary buckwheat is highly valued for its abundant rutin (quercetin 3-O-rutinoside). As a flavonoid glycoside, rutin is synthesized with the crucial involvement of UDP-dependent glycosyltransferases (UGTs). However, the functions and transcriptional regulation of the UGT-encoded genes remain poorly understood. This study identified a key gene, FtUFGT163, potentially encoding flavonol 3-O-glucoside (1 → 6) rhamnosyltransferase in Tartary buckwheat through omics analysis and molecular docking methods. The recombinant FtUFGT163 expressed in Escherichia coli demonstrated the capacity to glycosylate isoquercetin into rutin. Overexpression of FtUFGT163 significantly enhanced the rutin content in Tartary buckwheat. Further investigation identified a novel bZIP transcription factor, FtGBF1, that enhances FtUFGT163 expression by binding to the G-box element within its promoter, thereby augmenting rutin biosynthesis. Additional molecular biology experiments indicated that the specific positive regulator of rutin, FtMYB5/6, could directly activate the FtGBF1 promoter. Collectively, this study elucidates a novel regulatory module, termed "FtMYB5/6-FtGBF1-FtUFGT163", which effectively coordinates the biosynthesis of rutin in Tartary buckwheat, offering insights into the genetic enhancement of nutraceutical components in crops.

Tartary buckwheat rutin: Accumulation, metabolic pathways, regulation mechanisms, and biofortification strategies

Rutin is a significant flavonoid with strong antioxidant property and various therapeutic effects. It plays a crucial role in disease prevention and human health maintenance, especially in anti-inflammatory, antidiabetic, hepatoprotective and cardiovascular effects. While many plants can synthesize and accumulate rutin, tartary buckwheat is the only food crop possessing high levels of rutin. At present, the rutin content (RC) is regarded as the key index for evaluating the nutritional quality of tartary buckwheat. Consequently, rutin has become the focus for tartary buckwheat breeders and has made considerable progress. Here, we summarize research on the rutin in tartary buckwheat in the past two decades, including its accumulation, biosynthesis and breakdown pathways, and regulatory mechanisms. Furthermore, we propose several strategies to increase the RC in tartary buckwheat seeds based on current knowledge. This review aims to provide valuable references for elevating the quality of tartary buckwheat in the future.

Co-expressed network analysis based on 289 transcriptome samples reveals methyl jasmonate-mediated gene regulatory mechanism of flavonoid compounds in Dendrobium catenatum

Flavonoids are momentous bioactive ingredients in orchid plant Dendrobium catenatum (D. catenatum), which are bioactive compounds with great medical and commercial potential. However, the accurate dissection of flavonoids profiling and their accumulation mechanism are largely unknown. In this study, methyl jasmonate (MeJA) treatment was used to investigate the change of flavonoids content and transcripts in two D. catenatum clones (A6 and B1). We identified 40 flavonoids using liquid chromatograph mass spectrometer (LC-MS). By weighted gene co-expressed network analysis (WGCNA) of flavonoids content and transcript expression of MeJA-treated samples, 37 hub genes were identified. Among them, DcCHIL, DcFLS, and DcDFR were highly correlation with two key transcription factors DcWRKY3/4 by correlation analysis of large-scale transcriptome data and above hub genes expression. Furthermore, transient overexpression of DcWRKY3/4 in tobacco leaves significantly increased the content of flavonoids. This study identified flavonoid profiling and built a new approach to mine regulatory mechanism of flavonoids in D. catenatum. These valuable flavonoids and gene resources will be key for understanding and harnessing natural flavonoids products in pharmaceuticals and foods industry of D. catenatum.

Tartary Buckwheat (Fagopyrum tataricum) FtTT8 Inhibits Anthocyanin Biosynthesis and Promotes Proanthocyanidin Biosynthesis

Tartary buckwheat (Fagopyrum tataricum) is an important plant, utilized for both medicine and food. It has become a current research hotspot due to its rich content of flavonoids, which are beneficial for human health. Anthocyanins (ATs) and proanthocyanidins (PAs) are the two main kinds of flavonoid compounds in Tartary buckwheat, which participate in the pigmentation of some tissue as well as rendering resistance to many biotic and abiotic stresses. Additionally, Tartary buckwheat anthocyanins and PAs have many health benefits for humans and the plant itself. However, little is known about the regulation mechanism of the biosynthesis of anthocyanin and PA in Tartary buckwheat. In the present study, a bHLH transcription factor (TF) FtTT8 was characterized to be homologous with AtTT8 and phylogenetically close to bHLH proteins from other plant species. Subcellular location and yeast two-hybrid assays suggested that FtTT8 locates in the nucleus and plays a role as a transcription factor. Complementation analysis in Arabidopsis tt8 mutant showed that FtTT8 could not recover anthocyanin deficiency but could promote PAs accumulation. Overexpression of FtTT8 in red-flowering tobacco showed that FtTT8 inhibits anthocyanin biosynthesis and accelerates proanthocyanidin biosynthesis. QRT-PCR and yeast one-hybrid assay revealed that FtTT8 might bind to the promoter of NtUFGT and suppress its expression, while binding to the promoter of NtLAR and upregulating its expression in K326 tobacco. This displayed the bidirectional regulating function of FtTT8 that negatively regulates anthocyanin biosynthesis and positively regulates proanthocyanidin biosynthesis. The results provide new insights on TT8 in Tartary buckwheat, which is inconsistent with TT8 from other plant species, and FtTT8 might be a high-quality gene resource for Tartary buckwheat breeding.

Identification and Characterization of CtUGT3 as the Key Player of Astragalin Biosynthesis in Carthamus tinctorius L

Safflower (Carthamus tinctorius L.) is a multipurpose economic crop that is distributed worldwide. Flavonoid glycosides are the main bioactive components in safflower, but only a few UDP-glycosyltransferases (UGT) have been identified. Three differentially expressed UGT genes related with the accumulation of 9 flavonoid O-glycosides were screened from metabolomics and transcriptome analysis. Safflower corolla protoplasts were used to confirm the glycosylation ability of UGT candidates in vivo for the first time. The astragalin content was significantly increased only when CtUGT3 was overexpressed. CtUGT3 also showed flavonoid 3-OH and 7-OH glycosylation activities in vitro. Molecular modeling and site-directed mutagenesis revealed that G15, T136, S276, and E384 were critical catalytic residues for the glycosylation ability of CtUGT3. These results demonstrate that CtUGT3 has a flavonoid 3-OH glycosylation function and is involved in the biosynthesis of astragalin in safflower. This study provides a reference for flavonoid biosynthesis genes research in nonmodel plants.

Genome-Wide Identification of Histone Deacetylases and Their Roles Related with Light Response in Tartary Buckwheat (Fagopyrum tataricum)

Histone deacetylases (HDACs), known as histone acetylation erasers, function crucially in plant growth and development. Although there are abundant reports focusing on HDACs of Arabidopsis and illustrating their important roles, the knowledge of HDAC genes in Tartary buckwheat (Polygonales Polygonaceae Fagopyrum tataricum (L.) Gaertn) is still scarce. In the study, a total of 14 HDAC genes were identified and divided into three main groups: Reduced Potassium Dependency-3/His-52 tone Deacetylase 1 (RPD3/HDA1), Silent Information Regulator 2 (SIR2), and the plant-53 specific HD2. Domain and motif composition analysis showed there were conserved domains and motifs in members from the same subfamilies. The 14 FtHDACs were distributed asymmetrically on 7 chromosomes, with three segmental events and one tandem duplication event identified. The prediction of the cis-element in promoters suggested that FtHDACs probably acted in numerous biological processes including plant growth, development, and response to environmental signals. Furthermore, expression analysis based on RNA-seq data displayed that all FtHDAC genes were universally and distinctly expressed in diverse tissues and fruit development stages. In addition, we found divergent alterations in FtHDACs transcript abundance in response to different light conditions according to RNA-seq and RT-qPCR data, indicating that five FtHDACs might be involved in light response. Our findings could provide fundamental information for the HDAC gene family and supply several targets for future function analysis of FtHDACs related with light response of Tartary buckwheat.

Impact of Light and Dark Treatment on Phenylpropanoid Pathway Genes, Primary and Secondary Metabolites in Agastache rugosa Transgenic Hairy Root Cultures by Overexpressing Arabidopsis Transcription Factor AtMYB12

Agastache rugosa, otherwise called Korean mint, has a wide range of medicinal benefits. In addition, it is a rich source of several medicinally valuable compounds such as acacetin, tilianin, and some phenolic compounds. The present study aimed to investigate how the Tartary buckwheat transcription factor AtMYB12 increased the primary and secondary metabolites in Korean mint hairy roots cultured under light and dark conditions. A total of 50 metabolites were detected by using high-performance liquid chromatography (HPLC) and gas chromatography-time-of-flight mass spectrometry (GC-TOFMS). The result showed that the AtMYB12 transcription factor upregulated the phenylpropanoid biosynthesis pathway genes, which leads to the highest accumulation of primary and secondary metabolites in the AtMYB12-overexpressing hairy root lines (transgenic) than that of the GUS-overexpressing hairy root line (control) when grown under the light and dark conditions. However, when the transgenic hairy root lines were grown under dark conditions, the phenolic and flavone content was not significantly different from that of the control hairy root lines. Similarly, the heat map and hierarchical clustering analysis (HCA) result showed that most of the metabolites were significantly abundant in the transgenic hairy root cultures grown under light conditions. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) showed that the identified metabolites were separated far based on the primary and secondary metabolite contents present in the control and transgenic hairy root lines grown under light and dark conditions. Metabolic pathway analysis of the detected metabolites showed 54 pathways were identified, among these 30 were found to be affected. From these results, the AtMYB12 transcription factor activity might be light-responsive in the transgenic hairy root cultures, triggering the activation of the primary and secondary metabolic pathways in Korean mint.

UPLC-QTOF-MS-based metabolomics and chemometrics studies of geographically diverse Acer truncatum leaves: A traditional herbal tea in Northern China

Traditionally in Northern China, Acer truncatum leaves (ATL) have been used as herbal tea, now consumed worldwide. Few studies have reported ATL metabolites from different areas and their correlation with the environment. Thus, metabolomic analyses were conducted on ATL collected from twelve locations throughout four environmental zones in Northern China to understand the phytochemical differences with regards to environmental conditions. Sixty-four compounds, mostly flavonoids (FLAs) and gallic acid-containing natural products (GANPs), were characterized, including 34 previously unreported constituents from A. truncatum. Twenty-two markers were useful to differentiate ATL from the four environmental zones. Humidity, temperature, and sunshine duration are the predominant factors affecting FLAs and GANPs levels. Sunshine duration was positively correlated with eriodictyol (r = 0.994, p < 0.01), and humidity negatively with epicatechin gallate (r = -0.960, p < 0.05). These findings provide insights into ATL phytochemistry, aiding cultivation of A. truncatum tea with higher potential health benefits.

Light plays a critical role in the accumulation of chlorogenic acid in Lonicera macranthoides Hand.-Mazz

Light has important effects on plant metabolism. However, the relationship between the chlorogenic acid (CGA) content and light in plants remains unclear. Here, we investigated the effects of shading treatment on gene expression and CGA content in Lonicera macranthoides Hand.-Mazz. (LM), a widely used medicinal plant. A total of 1891 differentially expressed genes (DEGs) were obtained in flower buds and 819 in leaves in response to light in shading treatment compared to the control sample by RNA-Seq. After shading treatment, the content of CGA in LM leaves decreased significantly by 1.78-fold, the carotenoid content increased, and the soluble sugar and starch contents significantly decreased. WGCNA and the expression of related genes verified by qRT‒PCR revealed that CGA synthesis pathway enzyme genes form a co-expression network with genes for carbohydrate synthesis, photosynthesis, light signalling elements, and transcription factor genes (TFs) that affect the accumulation of CGA. Through a virus-induced gene silencing (VIGS) system and CGA assay in Nicotiana benthamiana (NB), we determined that downregulation of NbHY5 expression decreased the CGA content in NB leaves. In this study, we found that light provides energy and material for the accumulation of CGA in LM, and light affects the expression of CGA accumulation-related genes. Our results show that different light intensities have multiple effects on leaves and flower buds in LM and are able to coregulate LmHY5 expression and CGA synthesis.

Comparative transcriptome and genome analysis unravels the response of Tatary buckwheat root to nitrogen deficiency

Tartary buckwheat (Fagopyrum tataricum Garetn.), a dicotyledonous herbaceous crop, has good adaptation to low nitrogen (LN) condition. The plasticity of roots drives the adaption of Tartary buckwheat under LN, but the detailed mechanism behind the response of TB roots to LN remains unclear. In this study, the molecular mechanism of two Tartary buckwheat genotypes' roots with contrasting sensitivity in response to LN was investigated by integrating physiological, transcriptome and whole-genome re-sequencing analysis. LN improved primary and lateral root growth of LN-sensitive genotype, whereas the roots of LN-insensitive genotype showed no response to LN. 2, 661 LN-responsive differentially expressed genes (DEGs) were identified by transcriptome analysis. Of these genes, 17 N transport and assimilation-related and 29 hormone biosynthesis and signaling genes showed response to LN, and they may play important role in Tartary buckwheat root development under LN. The flavonoid biosynthetic genes' expression was improved by LN, and their transcriptional regulations mediated by MYB and bHLH were analyzed. 78 transcription factors, 124 small secreted peptides and 38 receptor-like protein kinases encoding genes involved in LN response. 438 genes were differentially expressed between LN-sensitive and LN-insensitive genotypes by comparing their transcriptome, including 176 LN-responsive DEGs. Furthermore, nine key LN-responsive genes with sequence variation were identified, including FtNRT2.4, FtNPF2.6 and FtMYB1R1. This paper provided useful information on the response and adaptation of Tartary buckwheat root to LN, and the candidate genes for breeding Tartary buckwheat with high N use efficiency were identified.

Effect of light quality on polyphenol biosynthesis in three varieties of mung bean sprouts with different color seed coats

We investigated the mechanism of the effect of different light qualities on the synthesis and regulation of mung bean sprouts. Light quality acts as a signal molecule, strongly enhancing polyphenol biosynthesis in sprouts. Mung bean (Vigna radiata) sprouts are a popular sprouting vegetable all over the world and are an excellent source of polyphenols with high antioxidant activity. This study investigated the effects of light qualities on the kinetic changes and metabolic regulation mechanism of light signal-mediating polyphenols in three mung bean sprout cultivars. Experimental results showed that three light qualities significantly enhanced the contents of caffeic acid, rutin, vitexin, genistin and delphinidin 3-glucoside. Interestingly, ferulic acid and vitexin responded selectively to blue light and red light, severally. Most genes involved in polyphenol biosynthesis were activated under different light quality conditions, resulting in an overaccumulation of phenylpropanoids. Pearson correlation analysis showed that PAL, F3H, F3'H and F3'5'H expression correlated highly with rutin, whereas ANS expression paralleled anthocyanin biosynthesis. Moreover, MYB111, MYB3, MYB4, MYB1 and MYC2 were critical regulators of polyphenol biosynthesis in mung bean sprouts. These changes were likely due to the changes in the expression of the photoreceptor genes CRY-D, PHOT2, PHYE and light response genes (PIF3 and HY5). Our results provide insights into polyphenol biosynthesis in sprouts and microgreens.

An R2R3-MYB FtMYB11 from Tartary buckwheat has contrasting effects on abiotic tolerance in Arabidopsis

R2R3-MYB transcription factors play important roles in response to abiotic stresses in planta, such as salt, drought, and osmotic stress. However, the role of FtMYB11 in Tartary buckwheat (Fagopyrum tataricum) in drought and osmotic tolerance has not yet been elucidated. In this study, we found that FtMYB11 was markedly induced by exogenous abscisic acid (ABA), salinity, and mannitol. Further, FtMYB11-overexpressing Arabidopsis showed hypersensitivity to ABA-mediated seed germination and seedling establishment through regulating transcripts of AtCBF1, AtDREB2A, and AtRD20, compared with wild type, indicating that FtMYB11 plays a positive role in ABA signaling. In contrast, transgenic lines overexpressing FtMYB11 were sensitive to mannitol and NaCl treatments, suggesting that FtMYB11 plays a negative role in osmotic tolerance. Intriguingly, the transcripts of ABA biosynthetic enzyme genes were significantly elevated in plants overexpressing FtMYB11 after exposure to osmotic stresses, such as AtABA3 and AtNCED3. In addition, flavonoid biosynthesis genes were also upregulated in transgenic Arabidopsis under ABA, salt, and drought treatments, including AtC4H, AtF3H, AtANS, AtFLS, and At4CL. The drought tolerance assay showed that plants overexpressing FtMYB11 displayed greater tolerance to water deficit through regulating MDA and proline content. Taken together, FtMYB11 has opposite roles in response to abiotic stresses, but it may mediate flavonoid biosynthesis through regulation of related enzyme genes.

A transcriptional complex of FtMYB102 and FtbHLH4 coordinately regulates the accumulation of rutin in Fagopyrum tataricum

Tartary buckwheat is rich in flavonoids, which not only play an important role in the plant-environment interaction, but are also beneficial to human health. Rutin is a therapeutic flavonol which is massively accumulated in Tartary buckwheat. It has been demonstrated that transcription factors control rutin biosynthesis. However, the transcriptional regulatory network of rutin is not fully clear. In this study, through transcriptome and target metabolomics, we validated the role of FtMYB102 and FtbHLH4 TFs at the different developmental stages of Tartary buckwheat. The elevated accumulation of rutin in the sprout appears to be closely associated with the expression of FtMYB102 and FtbHLH4. Yeast two-hybrid, transient luciferase activity and co-immunoprecipitation demonstrated that FtMYB102 and FtbHLH4 can interact and form a transcriptional complex. Moreover, yeast one-hybrid showed that both FtMYB102 and FtbHLH4 directly bind to the promoter of chalcone isomerase (CHI), and they can coordinately induce CHI expression as shown by transient luciferase activity assay. Finally, we transferred FtMYB102 and FtbHLH4 into the hairy roots of Tartary buckwheat and found that they both can promote the accumulation of rutin. Our results indicate that FtMYB102 and FtbHLH4 can form a transcriptional complex by inducing CHI expression to coordinately promote the accumulation of rutin.

Comparative proteomic analyses of Tartary buckwheat (Fagopyrum tataricum) seeds at three stages of development

Tartary buckwheat is among the valuable crops, utilized as both food and Chinese herbal medicine. To uncover the accumulation dynamics of the main nutrients and their regulatory mechanism of Tartary buckwheat seeds, microscopic observations and nutrient analysis were conducted which suggested that starch, proteins as well as flavonoid gradually accumulated among seed development. Comparative proteomic analysis of rice Tartary buckwheat at three different developmental stages was performed. A total of 78 protein spots showed differential expression with 74 of them being successfully identified by MALDI-TOF/TOF MS. Among them, granule bound starch synthase (GBSS1) might be the critical enzyme that determines starch biosynthesis, while 11 S seed storage protein and vicilin seemed to be the main globulin and affect seed storage protein accumulation in Tartary buckwheat seeds. Two enzymes, flavanone 3-hydroxylase (F3H) and anthocyanidin reductase (ANR), involved in the flavonoid biosynthesis pathway were identified. Further analysis on the expression profiles of flavonoid biosynthetic genes revealed that F3H might be the key enzyme that promote flavonoid accumulation. This study provides insights into the mechanism of nutrition accumulation at the protein level in Tartary buckwheat seeds and may facilitate in the breeding and enhancement of Tartary buckwheat germplasm.

Light Intensity-A Key Factor Affecting Flavonoid Content and Expression of Key Enzyme Genes of Flavonoid Synthesis in Tartary Buckwheat

Tartary buckwheat, a polygonaceae family plant, is rich in abundant flavonoids, high-quality protein, and well-balanced essential amino acids. This study aimed to investigate the effects of climatic variables on the quality of Tartary buckwheat. In this study, six distinct types of Tartary buckwheat collected from the Sichuan Basin, Western Sichuan Plateau, and Yunnan-Guizhou Plateau in southwest China were chosen to investigate the impact of climatic conditions from the grain-filling stage to the harvest stage on the concentration of flavonoids and expression of key enzyme genes involved the synthesis of flavonoids. Meteorological data of three producing areas were collected from the China Meteorological Network, mainly including maximum temperature (Tmax), minimum temperature (Tmin), diurnal temperature difference (Tdif), and light intensity. Then, the contents of rutin, kaempferol-3-O-rutin glycoside, quercetin, and kaempferol in 30 batches of Tartary buckwheat from 6 varieties including Chuanqiao No. 1, Chuanqiao No. 2, Xiqiao No. 1, Xiqiao No. 2, Miqiao No. 1 and Di ku were determined by ultra performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Furthermore, the expression levels of phenylalanine ammonia lyase (PAL), 4-coumaric acid coenzyme A ligase (4CL), and anthocyanin synthase (ANS) in six kinds of Tartary buckwheat were detected by real-time polymerase chain reaction (PCR). The seed photos were processed by ImageJ processing software. The partial least squares method was used to analyze the correlation. As a result, light intensity can promote the accumulation of flavonoids and the expression of key enzyme genes. Miqiao No. 1, which grows in Liangshan Prefecture, Sichuan Province, has the highest light intensity and is the dominant variety with flavonoid content. More importantly, the expression levels of PAL and 4CL in the secondary metabolic pathway of flavonoids were positively correlated with the content of Tartary buckwheat flavonoids. Interestingly, the expression level of ANS was negatively correlated with the content of PAL, 4CL, and flavonoids. In addition, ANS is a key gene affecting the seed coat color of Tartary buckwheat. The higher the expression of ANS, the darker the seed coat color. These findings provide a theoretical basis and reference for the breeding of fine buckwheat varieties.

Metabolomic and Transcriptomic Analysis of Flavonoid Biosynthesis in Two Main Cultivars of Actinidia arguta Sieb.Zucc. Grown in Northern China

Actinidia arguta Sieb.Zucc. is a fruit that is rich in flavonoids. Nevertheless, details of flavonoid formation and the potential mechanism behind flavonoid biosynthesis have not previously been reported. In order to explore the biosynthetic regulation mechanism of flavonoids in A. arguta Sieb.Zucc., we conducted a combination of extensive targeted metabolite analysis and analyzed transcriptomes to determine the flavonoids present and the genes bound up with flavonoid biosynthesis in the two main cultivated varieties of A. arguta Sieb.Zucc. in Northern China. The maturity period is from August to September. A total of 118 flavonoids were found in fruits. Among them, 39 flavonoids were accumulated at significant levels after fruit ripening. Transcriptome analysis indicated that most flavonoid biosynthesis structural genes and certain regulatory genes exhibited differential expression between the two varieties. Correlation analysis of transcriptome and metabolite profiles showed that the ways of expression of 21 differentially expressed genes related to structure and regulation between the 2 varieties were more highly correlated with 7 flavonoids after fruit ripening. These results contribute to the development of A. arguta Sieb.Zucc. as a food and drug homologous functional food.

Genome-Wide Identification of MAPK, MAPKK, and MAPKKK Gene Families in Fagopyrum tataricum and Analysis of Their Expression Patterns Under Abiotic Stress

The mitogen-activated protein kinase (MAPK) cascade is a highly conserved signal transduction pathway, ubiquitous in eukaryotes, such as animals and plants. The MAPK cascade has a dominant role in regulating plant adaptation to the environment, such as through stress responses, osmotic adjustment, and processes that modulate pathogenicity. In the present study, the MAPK cascade gene family was identified in Fagopyrum tataricum (Tartary buckwheat), based on complete genome sequence data. Using phylogenetic tree, conservative motif, and chromosome location analyses, a total of 65 FtMAPK cascade genes, distributed on five chromosomes, were classified into three families: MAPK (n = 8), MAPKK (n = 1), and MAPKKK (n = 56). Transcriptome data from Tartary buckwheat seedlings grown under different light conditions demonstrated that, under blue and red light, the expression levels of 18 and 36 FtMAPK cascade genes were up-regulated and down-regulated, respectively. Through qRT-PCR experiments, it was observed that FtMAPK5, FtMAPKK1, FtMAPKKK8, FtMAPKKK10, and FtMAPKKK24 gene expression levels in the Tartary buckwheat seedlings increased under three types of abiotic stress: drought, salt, and high temperature. A co-expression network of FtMAPK cascade genes was constructed, based on gene expression levels under different light conditions, and co-expressed genes annotated by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, which identified numerous transcription factors related to plant abiotic stress. The authors conclude that FtMAPK cascade genes have important roles in the growth and development of Tartary buckwheat, as well as its responses to abiotic stress.

Environmental and Genetic Factors Involved in Plant Protection-Associated Secondary Metabolite Biosynthesis Pathways

Plant specialized metabolites (PSMs) play essential roles in the adaptation to harsh environments and function in plant defense responses. PSMs act as key components of defense-related signaling pathways and trigger the extensive expression of defense-related genes. In addition, PSMs serve as antioxidants, participating in the scavenging of rapidly rising reactive oxygen species, and as chelators, participating in the chelation of toxins under stress conditions. PSMs include nitrogen-containing chemical compounds, terpenoids/isoprenoids, and phenolics. Each category of secondary metabolites has a specific biosynthetic pathway, including precursors, intermediates, and end products. The basic biosynthetic pathways of representative PSMs are summarized, providing potential target enzymes of stress-mediated regulation and responses. Multiple metabolic pathways share the same origin, and the common enzymes are frequently to be the targets of metabolic regulation. Most biosynthetic pathways are controlled by different environmental and genetic factors. Here, we summarized the effects of environmental factors, including abiotic and biotic stresses, on PSM biosynthesis in various plants. We also discuss the positive and negative transcription factors involved in various PSM biosynthetic pathways. The potential target genes of the stress-related transcription factors were also summarized. We further found that the downstream targets of these Transcription factors (TFs) are frequently enriched in the synthesis pathway of precursors, suggesting an effective role of precursors in enhancing of terminal products. The present review provides valuable insights regarding screening targets and regulators involved in PSM-mediated plant protection in non-model plants.

Genome-wide characterization of nuclear factor Y transcription factors in Fagopyrum tataricum

The nuclear factor Y (NF-Y) is an important transcription factor family that regulates plant developmental processes and abiotic stress responses. Currently, genome-wide studies of the NF-Y family are limited in Fagopyrum tataricum, an important economic crop. Based on the released genome assembly, we predicted a total of 38 NF-Y encoding genes (FtNF-Ys), including 12 FtNF-YAs, 18 FtNF-YBs, and eight FtNF-YCs subunits, in F. tataricum. Phylogenetic tree and sequence alignments showed that FtNF-Ys were conserved between F. tataricum and other species. Tissue expressions and network analyses suggested that FtNF-Ys might be involved in regulating developmental processes in different tissues. Several FtNF-YAs and FtNF-Ybs were also potentially involved in light response. In addition, FtNF-YC-like1 and FtNF-YC-like2 partially rescued the late flowering phenotype in nf-yc1 nf-yc3 nf-yc4 nf-yc9 (ycQ) mutant in Arabidopsis thaliana, supporting a conserved role of FtNF-Ys in regulating developmental processes. Together, the genomic information provides a comprehensive understanding of the NF-Y transcription factors in F. tataricum, which will be useful for further investigation of their functions in F. tataricum.

Different Phenylalanine Pathway Responses to Cold Stress Based on Metabolomics and Transcriptomics in Tartary Buckwheat Landraces

Tartary buckwheat (Fagopyrum tataricum) is strongly adapted to growth in adverse environments. In Liangshan, the Yi people cultivate different Tartary buckwheat landraces in different habitats. In this study, we aimed to understand the molecular differences in transcriptomic and metabolomic responses underlying cold tolerance between two Tartary buckwheat landraces (TM and RG) cultivated at different altitudes. After cold treatment, TM showed normal growth in the seedling stage and had significantly higher total flavonoids (16.53 mg/g, 1.47 times), rutin (5.73 mg/g, 1.32 times), and quercetin (0.08 mg/g, 2.67 times), which were higher than those in RG. In addition, TM showed higher-level changes in carbon and nitrogen metabolism than RG. Combined transcriptome and metabolomic analyses showed that phenylpropanoid biosynthesis was upregulated after cold treatment, and in TM, rutin synthesis was upregulated with a higher-level response to cold stress. RG showed higher expression in anthocyanins in response to cold stress. In addition, 24 structural genes involved in flavonoid synthesis, including 6 PAL, 3 C4H, 2 4CL, 2 CHS, 1 CHI, 3 F3H, 3 DFR, 1 FLS, 1 F3'H, and 4 GTR genes, were identified. These results will provide sufficient information for breeding Tartary buckwheat with high cold tolerance and constructing rutin high-yield varieties based on genetic engineering.

Integrated Transcriptomics and Widely Targeted Metabolomics Analyses Provide Insights Into Flavonoid Biosynthesis in the Rhizomes of Golden Buckwheat (Fagopyrum cymosum)

Golden buckwheat (Fagopyrum cymosum) is used in Traditional Chinese Medicine. It has received attention because of the high value of its various medicinal and nutritional metabolites, especially flavonoids (catechin and epicatechin). However, the metabolites and their encoding genes in golden buckwheat have not yet been identified in the global landscape. This study performed transcriptomics and widely targeted metabolomics analyses for the first time on rhizomes of golden buckwheat. As a result, 10,191 differentially expressed genes (DEGs) and 297 differentially regulated metabolites (DRMs) were identified, among which the flavonoid biosynthesis pathway was enriched in both transcriptome and metabolome. The integration analyses of the transcriptome and the metabolome revealed a network related to catechin, in which four metabolites and 14 genes interacted with each other. Subsequently, an SG5 R2R3-MYB transcription factor, named FcMYB1, was identified as a transcriptional activator in catechin biosynthesis, as it was positively correlated to eight flavonoid biosynthesis genes in their expression patterns and was directly bound to the promoters of FcLAR2 and FcF3'H1 by yeast one hybrid analysis. Finally, a flavonoid biosynthesis pathway was proposed in the rhizomes of golden buckwheat, including 13 metabolites, 11 genes encoding 9 enzymes, and 1 MYB transcription factor. The expression of 12 DEGs were validated by qRT-PCR, resulting in a good agreement with the Pearson R ranging from 0.83 to 1. The study provided a comprehensive flavonoid biosynthesis and regulatory network of golden buckwheat.

Transcriptome sequencing and metabolomics analyses provide insights into the flavonoid biosynthesis in Torreya grandis kernels

The kernel of Torreya grandis (T. grandis) is a rare nut with a variety of bioactive compounds. Flavonoids are a very important class of bioactive compounds with high antioxidant activity in T. grandis kernels. However, the flavonoid compositions which mainly contribute to antioxidant capacity and the molecular basis of flavonoid biosynthesis in T. grandis remain unclear. Here, transcriptome sequencing and metabolomics analysis for kernels were performed. In total, 124 flavonoids were identified. Among them, 9 flavonoids were highly correlated with antioxidant activity. Furthermore, unigenes encoding CHS, DFR and ANS showed significant correlation with the 9 flavonoids. Transient overexpression of TgDFR1 in tobacco leaves resulted in increased antioxidant activity. Moreover, several transcription factors from MYB, bHLH and bZIP families were identified by co-expression assay, suggesting that they may regulate flavonoid biosynthesis. Our findings provide a molecular basis and new insights into the flavonoid biosynthesis in T. grandis kernels.

Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L

Artemisinin is currently the most effective ingredient in the treatment of malaria, which is thus of great significance to study the genetic regulation of Artemisia annua. Alternative splicing (AS) is a regulatory process that increases the complexity of transcriptome and proteome. The most common mechanism of alternative splicing (AS) in plant is intron retention (IR). However, little is known about whether the IR isoforms produced by light play roles in regulating biosynthetic pathways. In this work we would explore how the level of AS in A. annua responds to light regulation. We obtained a new dataset of AS by analyzing full-length transcripts using both Illumina- and single molecule real-time (SMRT)-based RNA-seq as well as analyzing AS on various tissues. A total of 5,854 IR isoforms were identified, with IR accounting for the highest proportion (48.48%), affirming that IR is the most common mechanism of AS. We found that the number of up-regulated IR isoforms (1534/1378, blue and red light, respectively) was more than twice that of down-regulated (636/682) after treatment of blue or red light. In the artemisinin biosynthetic pathway, 10 genes produced 16 differentially expressed IR isoforms. This work demonstrated that the differential expression of IR isoforms induced by light has the potential to regulate sesquiterpenoid biosynthesis. This study also provides high accuracy full-length transcripts, which can be a valuable genetic resource for further research of A. annua, including areas of development, breeding, and biosynthesis of active compounds.

Genome-wide analysis of BBX gene family in Tartary buckwheat (Fagopyrum tataricum)

BBX (B-box), a zinc finger transcription factor with one or two B-box domains, plays an important role in plant photomorphogenesis, growth, and development as well as response to environmental changes. In this study, 28 Tartary buckwheat BBX (FtBBX) genes were identified and screened using a comparison program. Their physicochemical properties, gene structures, conserved motifs, distribution in chromosomal, and phylogeny of the coding proteins, as well as their expression patterns, were analyzed. In addition, multiple collinearity analysis in three monocots and three dicot species illustrated that the BBX proteins identified from monocots clustered separately from those of dicots. Moreover, the expression of 11 candidate BBX genes with probable involvement in the regulation of anthocyanin biosynthesis was analyzed in the sprouts of Tartary buckwheat during light treatment. The results of gene structure analysis showed that all the 28 BBX genes contained B-box domain, three genes lacked introns, and these genes were unevenly distributed on the other seven chromosomes except for chromosome 6. The 28 proteins contained 10 conserved motifs and could be divided into five subfamilies. BBX genes of Tartary buckwheat showed varying expression under different conditions demonstrating that FtBBXs might play important roles in Tartary buckwheat growth and development. This study lays a foundation for further understanding of Tartary buckwheat BBX genes and their functions in growth and development as well as regulation of pigmentation in Tartary buckwheat.

Effects of Light on Secondary Metabolite Biosynthesis in Medicinal Plants

Secondary metabolites (SMs) found in medicinal plants are one of main sources of drugs, cosmetics, and health products. With the increase in demand for these bioactive compounds, improving the content and yield of SMs in medicinal plants has become increasingly important. The content and distribution of SMs in medicinal plants are closely related to environmental factors, especially light. In recent years, artificial light sources have been used in controlled environments for the production and conservation of medicinal germplasm. Therefore, it is essential to elucidate how light affects the accumulation of SMs in different plant species. Here, we systematically summarize recent advances in our understanding of the regulatory roles of light quality, light intensity, and photoperiod in the biosynthesis of three main types of SMs (polyphenols, alkaloids, and terpenoids), and the underlying mechanisms. This article provides a detailed overview of the role of light signaling pathways in SM biosynthesis, which will further promote the application of artificial light sources in medicinal plant production.

Characterization of abscisic acid (ABA) receptors and analysis of genes that regulate rutin biosynthesis in response to ABA in Fagopyrum tataricum

Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is a nutritional crop, which has high rutin, and is good for health. Until now, plant genetic engineering is insufficient for Tartary buckwheat. Abscisic acid (ABA), as one of phytohormones, is involved in the regulation of plant growth and development, and responses to diverse environmental challenges. Although ABA receptors have been well characterized in Arabidopsis, it is little understood in Tartary buckwheat. In this study, we identified 12 ABA receptors, designated as FtRCAR1 through FtRCAR12 in Tartary buckwheat. FtRCARs are divided into three subfamily. Based on the similarity, we could predict that FtRCARs comprise of the monomeric (FtRCAR1, 3, 4, 5, 9, 10, 11 and 12) and the dimeric (FtRCAR2, 7 and 8) state in solution. The analysis of the transcript pattern indicated that most of FtRCARs were significantly variable among the root, stem, leaf, flower and seed, while FtRCAR4 transcript was undetectable under in all tissues. The transcript levels of FtRCARs under ABA treatment indicated that most FtRCARs transcripts were depressed, indicating a possible feedback regulation of ABA signaling. The analysis of rutin biosynthesis related-genes indicated that ABA up-graduated CHS, CHI, F3'H, F3H and FLS transcript levels, while transcripts of 4CL and PAL were down-regulated. In addition, the transcription factors that mediated the rutin biosynthesis related-genes were also regulated by exogenous ABA. Thus, the identification and the characterization of FtRCARs would enable us to further understand the role of ABA signal in Tartary buckwheat.

FtMYB6, a Light-Induced SG7 R2R3-MYB Transcription Factor, Promotes Flavonol Biosynthesis in Tartary Buckwheat (Fagopyrum tataricum)

Tartary buckwheat (Fagopyrum tataricum) is rich in flavonols, which are thought to be highly beneficial for human health. However, little is known about the regulatory mechanism of flavonol biosynthesis in Tartary buckwheat. In this study, we identified and characterized a novel SG7 R2R3-MYB transcription factor in Tartary buckwheat, FtMYB6. We showed that FtMYB6 is located in the nucleus and acts as a transcriptional activator. The FtMYB6 promoter showed strong spatiotemporal specificity and was induced by light. The expression of FtMYB6 showed a significant correlation with rutin accumulation in the roots, stems, leaves, and flowers. Overexpression of FtMYB6 in transgenic Tartary buckwheat hairy roots and tobacco (Nicotiana tabacum) plants significantly increased the accumulation of flavonols. In transient luciferase (LUC) activity assay, FtMYB6 promoted the activity of FtF3H and FtFLS1 promoters and inhibited the activity of the Ft4CL promoter. Collectively, our results suggest that FtMYB6 promotes flavonol biosynthesis by activating FtF3H and FtFLS1 expression.

Genome-wide analyses reveals a glucosyltransferase involved in rutin and emodin glucoside biosynthesis in tartary buckwheat

With people's increasing needs for health concern, rutin and emodin in tartary buckwheat have attracted much attention for their antioxidant, anti-diabetic and reducing weight function. However, the biosynthesis of rutin and emodin in tartary buckwheat is still unclear; especially their later glycosylation contributing to make them more stable and soluble is uncovered. Based on tartary buckwheat' genome, the gene structures of 106 UGTs were analyzed; 21 candidate FtUGTs were selected to enzymatic test by comparing their transcript patterns. Among them, FtUGT73BE5 and other 4 FtUGTs were identified to glucosylate flavonol or emodin in vitro; especially rFtUGT73BE5 could catalyze the glucosylation of all tested flavonoids and emodin. Furthermore, the identical in vivo functions of FtUGT73BE5 were demonstrated in tartary buckwheat hairy roots. The transcript profile of FtUGT73BE5 was consistent with the accumulation trend of rutin in plant; this gene may relate to anti-adversity for its transcripts were up-regulated by MeJA, and repressed by ABA.

Bioinformatics-assisted, integrated omics studies on medicinal plants

The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.

Metabolite Profiling and Transcriptome Analyses Provide Insights into the Flavonoid Biosynthesis in the Developing Seed of Tartary Buckwheat (Fagopyrum tataricum)

Tartary buckwheat (Fagopyrum tataricum) seeds are rich in flavonoids. However, the detailed flavonoid compositions and the molecular basis of flavonoid biosynthesis in tartary buckwheat seeds remain largely unclear. Here, we performed a combined metabolite profiling and transcriptome analysis to identify flavonoid compositions and characterize genes involved in flavonoid biosynthesis in the developing tartary buckwheat seeds. In total, 234 flavonoids, including 10 isoflavones, were identified. Of these, 80 flavonoids were significantly differential accumulation during seed development. Transcriptome analysis indicated that most structural genes and some potential regulatory genes of flavonoid biosynthesis were significantly differentially expressed in the course of seed development. Correlation analysis between transcriptome and metabolite profiling shown that the expression patterns of some differentially expressed structural genes and regulatory genes were more consistent with the changes in flavonoids profiles during seed development and promoted one SG7 subgroup R2R3-MYB transcription factors (FtPinG0009153900.01) was identified as the key regulatory gene of flavonoid biosynthesis. These findings provide valuable information for understanding the mechanism of flavonoid biosynthesis in tartary buckwheat seeds and the further development of tartary buckwheat health products.