Comparative Transcriptome and Metabolic Profiling Analysis of Buckwheat (Fagopyrum Tataricum (L.) Gaertn.) under Salinity Stress

Advancements in multi-omics for nutraceutical enhancement and traits improvement in buckwheat

Buckwheat (Fagopyrum spp.) is a typical pseudocereal, valued for its extensive nutraceutical potential as well as its centuries-old cultivation. Tartary buckwheat and common buckwheat have been used globally and become well-known nutritious foods due to their high quantities of: proteins, flavonoids, and minerals. Moreover, its increasing demand makes it critical to improve nutraceutical, traits and yield. In this review, bioactive compounds accumulated in buckwheat were comprehensively evaluated according to their chemical structure, properties, and physiological function. Biosynthetic pathways of flavonoids, phenolic acids, and fagopyrin were methodically summarized, with the regulation of flavonoid biosynthesis. Although there are classic synthesis pathways presented in the previous research, the metabolic flow of how these certain compounds are being synthesized in buckwheat still remains uncovered. The functional genes involved in the biosynthesis of flavonols, stress response, and plant development were identified based on multi-omics research. Furthermore, it delves into the applications of multi-omics in improving buckwheat's agronomic traits, including: yield, nutritional content, stress resilience, and bioactive compounds biosynthesis. While pangenomics combined with other omics to mine elite genes, the regulatory network and mechanism of specific agronomic traits and biosynthetic of bioactive components, and developing a more efficient genetic transformation system for genetic engineering require further investigation for the execution of breeding designs aimed at enhancing desirable traits in buckwheat. This critical review will provide a comprehensive understanding of multi-omics for nutraceutical enhancement and traits improvement in buckwheat.

Understanding salinity tolerance mechanisms in finger millet through metabolomics

Finger millet (Eleusine coracana Gaertn L.) is an underutilized but nutritionally rich climate resilient food crop that is generally cultivated on marginal lands. Soil salinization is a major abiotic stress that leads to a reduction in growth and yield by affecting various physiological and metabolic processes in plants. The existence of genotypic variation for salt tolerance in finger millet indicates the possibility of crop improvement via plant breeding. The overall objective of the study was to identify metabolic changes associated with improved salt tolerance in finger millet. Understanding tolerance mechanisms plays a pivotal role in the development of elite cultivars. Based on the consensus of several phenotypic data at the germination and seedling stages, we further evaluated two accessions (IE 518 and IE 405) with morphophysiological parameters and metabolomics to dissect the salinity tolerance mechanisms in finger millet. Significant phenotypic separation of IE 518 and IE 405 for salt tolerance was reflected through differences in several physiological processes such as maximum quantum yield of photosystem II (FV/FM), net photosynthesis rate (Pn), shoot Na+ ion accumulation, and oxidative stresses (electrolyte leakage and malondialdehyde content). However, both accessions showed retention of K+ ions, which underscores the role of ion homeostasis in finger millet. Pathway enrichment analysis with the uniquely salt regulated metabolites identified key metabolic pathways such as stress signaling, biotin metabolism, energy metabolism, amino acid biosynthesis, and sugar metabolism in IE 518. An enhanced accumulation of reducing sugars (mannose and melibiose) and amino acids (L-Proline and GABA) in IE 518 under salinity suggests maintaining osmotic balance as a key tolerance mechanism in finger millet.

Rutin distribution in Tartary buckwheat: Identifying prime dietary sources through comparative analysis of post-processing treatments

Rutin is a crucial bioactive compound that determines the nutritional value of Tartary buckwheat (TB). However, the potential of utilizing TB as a dietary source of rutin for human consumption remains largely unexplored. This study aims to address these knowledge gaps by conducting a detailed analysis of rutin content distribution in TB tissues. Our findings revealed a significant variation in rutin content across different plant tissues. Notably, higher levels of rutin were found in embryos and cotyledons compared to other tissues, highlighting them as the primary sites of rutin accumulation in TB seeds and sprouts. Additional research on the processing of TB showed that sprouts and seeds retain high rutin levels even after boiling, steaming, deep-frying, stir-frying, and popping. Comparative analysis of different TB-derived products confirmed that cooked seeds and sprouts can serve as significant dietary sources of rutin. This study offers a foundational framework for the development of future dietary recommendations and applications of TB.

Elucidating the wedelolactone biosynthesis pathway from Eclipta prostrata (L.) L.: a comprehensive analysis integrating de novo comparative transcriptomics, metabolomics, and molecular docking of targeted proteins

Eclipta prostrata belongs to the Asteraceae family. The plant contains bioactive compounds like wedelolactone (WDL) and demethylwedelolactone (DW). Its transcriptomic information engaged with secondary metabolite biosynthesis is not available. Based on differential accumulation of WDL and DW in root, shoot of the mature plant, we performed comparative de novo transcriptome of root and shoot tissue in three independent biological replicates and generated 49820 unique transcripts. Annotation resulted in significant matches for 43,015 unigenes. Based on differential gene expression data, we found WDL biosynthesis-related transcripts, which were mainly upregulated in shoot. Finally, 13 selected differentially expressed transcripts related to WDL biosynthesis that were validated by qRT-PCR. Detailed tissue-specific metabolite and transcript profiling revealed that DW highly accumulated in root and WDL accumulation was high in aerial part along with transcripts. For WDL pathway exploration, we did integrated profiling of 08 metabolites and 13 transcripts and witnessed that only naringenin, apigenin, DW, and WDL were detected in different developmental stages. Taking leads from the findings, we postulated that naringenin to apigenin pathway is one potential route for WDL biosynthesis. Moreover, wound stress led to accumulation of DW and WDL and related biosynthetic transcripts. Furthermore, the selected enzymes were subjected to molecular docking and binding studies for the predicted substrates involved in crucial and advance steps of WDL biosynthesis. A comprehensive analysis integrating de novo transcriptomics, metabolomics, and molecular docking of targeted proteins paves the way for the elucidation of the putative wedelolactone biosynthesis pathway from E. prostrata.

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.

Germplasm Resources and Metabolite Marker Screening of High-Flavonoid Tartary Buckwheat (Fagopyrum tataricum)

Tartary buckwheat is an annual minor cereal crop with a variety of secondary metabolites, endowing it with a high nutritional and medicinal value. Flavonoids constitute the primary compounds of Tartary buckwheat. Recently, metabolomics, as an adjunct breeding method, has been increasingly employed in crop research. This study explores the correlation between the total flavonoid content (TFC) and antioxidant capacity in 167 Tartary buckwheat varieties. Ten Tartary buckwheat varieties with significant differences in flavonoid content and antioxidant capacity were selected by cluster analysis. With the use of liquid chromatography-mass spectrometry, 58 flavonoid compounds were identified, namely, 42 flavonols, 10 flavanols, 3 flavanones, 1 isoflavone, 1 anthocyanidin, and 1 proanthocyanidin. Different samples were clearly separated by employing principal component analysis and partial least-squares discriminant analysis. Eight differential flavonoid compounds were further selected through volcano plots and variable importance in projection. Differential metabolites were highly correlated with TFC and antioxidant capacity. Finally, metabolic markers of kaempferol-3-O-hexoside, kaempferol-7-O-glucoside, and naringenin-O-hexoside were determined by the random forest model. The findings provide a basis for the selection and identification of Tartary buckwheat varieties with high flavonoid content and strong antioxidant activity.

Identification of Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn) and Common Buckwheat (Fagopyrum esculentum Moench) Using Gas Chromatography-Mass Spectroscopy-Based Untargeted Metabolomics

Tartary buckwheat has attracted more attention than common buckwheat due to its unique chemical composition and higher efficacy in the prevention of various diseases. The content of flavonoids in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn) is higher than that in common buckwheat (Fagopyrum esculentum Moench). However, the processing process of Tartary buckwheat is complex, and the cost is high, which leads to the frequent phenomenon of common buckwheat counterfeiting and adulteration in Tartary buckwheat, which seriously damages the interests of consumers and disrupts the market order. In order to explore a new and simple identification method for Tartary buckwheat and common buckwheat, this article uses metabolomics technology based on GC-MS to identify Tartary buckwheat and common buckwheat. The results show that the PLS-DA model can identify Tartary buckwheat and common buckwheat, as well as Tartary buckwheat from different regions, without an over-fitting phenomenon. It was also found that ascorbate and aldarate metabolism was the main differential metabolic pathway between Tartary buckwheat and common buckwheat, as well as the amino acids biosynthesis pathway. This study provides a new attempt for the identification of Tartary buckwheat and common buckwheat for the quality control of related agricultural products.

Unravelling Differential DNA Methylation Patterns in Genotype Dependent Manner under Salinity Stress Response in Chickpea

DNA methylation is one of the epigenetic mechanisms that govern gene regulation in response to abiotic stress in plants. Here, we analyzed the role of epigenetic variations by exploring global DNA methylation and integrating it with differential gene expression in response to salinity stress in tolerant and sensitive chickpea genotypes. Genome-wide DNA methylation profiles showed higher CG methylation in the gene body regions and higher CHH methylation in the TE body regions. The analysis of differentially methylated regions (DMRs) suggested more hyper-methylation in response to stress in the tolerant genotype compared to the sensitive genotype. We observed higher enrichment of CG DMRs in genes and CHH DMRs in transposable elements (TEs). A positive correlation of gene expression with CG gene body methylation was observed. The enrichment analysis of DMR-associated differentially expressed genes revealed they are involved in biological processes, such as lateral root development, transmembrane transporter activity, GTPase activity, and regulation of gene expression. Further, a high correlation of CG methylation with CHG and CHH methylation under salinity stress was revealed, suggesting crosstalk among the methylation contexts. Further, we observed small RNA-mediated CHH hypermethylation in TEs. Overall, the interplay between DNA methylation, small RNAs, and gene expression provides new insights into the regulatory mechanism underlying salinity stress response in chickpeas.

Metabolomic and transcriptomic changes in mungbean (Vigna radiata (L.) R. Wilczek) sprouts under salinity stress

Mungbean (Vigna radiata) sprouts are consumed globally as a healthy food with high nutritional values, having antioxidant and anticancer capacity. Under mild salinity stress, plants accumulate more secondary metabolites to alleviate oxidative stress. In this study, metabolomic and transcriptomic changes in mungbean sprouts were identified using a reference cultivar, sunhwa, to understand the regulatory mechanisms of secondary metabolites in response to salinity stress. Under salinity conditions, the contents of phenylpropanoid-derived metabolites, including catechin, chlorogenic acid, isovitexin, p-coumaric acid, syringic acid, ferulic acid, and vitexin, significantly increased. Through RNA sequencing, 728 differentially expressed genes (DEGs) were identified and 20 DEGs were detected in phenylpropanoid and flavonoid biosynthetic pathways. Among them, 11 DEGs encoding key enzymes involved in the biosynthesis of the secondary metabolites that increased after NaCl treatment were significantly upregulated, including dihydroflavonol 4-reductase (log₂FC 1.46), caffeoyl-CoA O-methyltransferase (1.38), chalcone synthase (1.15), and chalcone isomerase (1.19). Transcription factor families, such as MYB, WRKY, and bHLH, were also identified as upregulated DEGs, which play a crucial role in stress responses in plants. Furthermore, this study showed that mild salinity stress can increase the contents of phenylpropanoids and flavonoids in mungbean sprouts through transcriptional regulation of the key enzymes involved in the biosynthetic pathways. Overall, these findings will provide valuable information for molecular breeders and scientists interested in improving the nutritional quality of sprout vegetables.

FtUGT79A15 is responsible for rutinosylation in flavonoid diglycoside biosynthesis in Fagopyrum tataricum

Tartary buckwheat shows health benefits with its high antioxidant activity and abundant flavonoid content. However, glycosylated flavonoid accumulation patterns and their molecular basis remain unidentified in Tartary buckwheat. Here, our metabolomics analysis revealed that F3'H branching was the major flavonoid metabolic flux in Tartary buckwheat. Interestingly, metabolome results also showed that the most abundant flavonoids were mainly in the glycosylated form, including flavonoid glycosides and flavonoid diglycosides in Tartary buckwheat. However, the flavonoid glycosides glycosyltransferase (GGT) gene catalyzing the second glycosylation step of flavonoid diglycoside has not been discovered yet in Tartary buckwheat. Thus, we explored GGT genes in the transcriptome-metabolome correlation network and confirmed that FtUGT79A15 showed the rhamnosyltransferase activity to catalyze quercetin 3-O-glucoside to rutin invitro and inplanta. Overall, FtUGT79A15 was identified to involve in the flavonoid diglycoside biosynthesis pathway in Tartary buckwheat.

Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement

Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.

Widely-Targeted Metabolic Profiling in Lycium barbarum Fruits under Salt-Alkaline Stress Uncovers Mechanism of Salinity Tolerance

Wolfberry (Lycium barbarum L.) is an important economic crop widely grown in China. The effects of salt-alkaline stress on metabolites accumulation in the salt-tolerant Ningqi1 wolfberry fruits were evaluated across 12 salt-alkaline stress gradients. The soil pH, Na+, K+, Ca2+, Mg2+, and HCO3− contents decreased at a gradient across the salt-alkaline stress gradients. Based on the widely-targeted metabolomics approach, we identified 457 diverse metabolites, 53% of which were affected by salt-alkaline stress. Remarkably, soil salt-alkaline stress enhanced metabolites accumulation in wolfberry fruits. Amino acids, alkaloids, organic acids, and polyphenols contents increased proportionally across the salt-alkaline stress gradients. In contrast, nucleic acids, lipids, hydroxycinnamoyl derivatives, organic acids and derivatives and vitamins were significantly reduced by high salt-alkaline stress. A total of 13 salt-responsive metabolites represent potential biomarkers for salt-alkaline stress tolerance in wolfberry. Specifically, we found that constant reductions of lipids and chlorogenic acids; up-regulation of abscisic acid and accumulation of polyamines are essential mechanisms for salt-alkaline stress tolerance in Ningqi1. Overall, we provide for the first time some extensive metabolic insights into salt-alkaline stress tolerance and key metabolite biomarkers which may be useful for improving wolfberry tolerance to salt-alkaline stress.

Integrative analysis of the pharmaceutical active ingredient and transcriptome of the aerial parts of Glycyrrhiza uralensis under salt stress reveals liquiritin accumulation via ABA-mediated signaling

The aerial parts of Glycyrrhiza uralensis supply substantial raw material for the extraction of active pharmaceutical ingredients comprehensively utilized in many industries. Our previous study indicated that salt stress increased the content of active ingredients. However, the regulatory mechanism remains unclear. In this study, RNA-sequencing (RNA-seq) of the aerial parts of G. uralensis treated with 150 mM NaCl for 0, 2, 6, and 12 h was performed to identify the key genes and metabolic pathways regulating pharmacological active component accumulation. The main active component detection showed that liquiritin was the major ingredient and exhibited more than a ten-fold significant increase in the 6 h NaCl treatment. Temporal expression analysis of the obtained 4245 differentially expressed genes (DEGs) obtained by RNA-seq revealed two screened profiles that included the significant up-regulated DEGs (UDEGs) at different treatment points. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these UDEGs identified phenylpropanoid metabolism and flavonoid biosynthesis as the most significantly enriched pathways in 2 h treated materials. Interestingly, the carotenoid biosynthesis pathway that is related to ABA synthesis was also discovered, and the ABA content was significantly promoted after 6 h NaCl treatment. Following ABA stimulation, the content of liquiritin demonstrated a significant and immediate increase after 2 h treatment, with the corresponding consistent expression of genes involved in the pathways of ABA signal transduction and flavonoid biosynthesis, but not in the pathway of glycyrrhizic acid biosynthesis. Our study concludes that salt stress might promote liquiritin accumulation through the ABA-mediated signaling pathway, and provides effective reference for genetic improvement and comprehensive utilization of G. uralensis.

Genome-wide identification of MAPK gene family members in Fagopyrum tataricum and their expression during development and stress responses

BACKGROUND

Mitogen-activated protein kinases (MAPKs) plays essential roles in the development, hormone regulation and abiotic stress response of plants. Nevertheless, a comprehensive study on MAPK family members has thus far not been performed in Tartary buckwheat.

RESULTS

Here, we identified 16 FtMAPKs in the Fagopyrum tataricum genome. Phylogenetic analysis showed that the FtMAPK family members could be classified into Groups A, B, C and D, in which A, B and C members contain a Thr-Glu-Tyr (TEY) signature motif and Group D members contain a Thr-Asp-Tyr (TDY) signature motif. Promoter cis-acting elements showed that most ProFtMAPks contain light response elements, hormone response elements and abiotic stress response elements, and several ProFtMAPks have MYB-binding sites, which may be involved in the regulation of flavonoid biosynthesis-related enzyme gene expression. Synteny analysis indicated that FtMAPKs have a variety of biological functions. Protein interaction prediction suggested that MAPKs can interact with proteins involved in development and stress resistance. Correlation analysis further confirmed that most of the FtMAPK genes and transcription factors involved in the stress response have the same expression pattern. The transient transformation of FtMAPK1 significantly increased the antioxidant enzymes activity in Tartary buckwheat leaves. In addition, we also found that FtMAPK1 can respond to salt stress by up-regulating the transcription abundance of downstream genes.

CONCLUSIONS

A total of 16 MAPKs were identified in Tartary buckwheat, and the members of the MAPK family containing the TDY motif were found to have expanded. The same subfamily members have relatively conserved gene structures and similar protein motifs. Tissue-specific expression indicated that the expression of all FtMAPK genes varied widely in the roots, stems, leaves and flowers. Most FtMAPKs can regulate the expression of other transcription factors and participate in the abiotic stress response. Our findings comprehensively revealed the FtMAPK gene family and laid a theoretical foundation for the functional characterization of FtMAPKs.

Integrative Analysis of the Transcriptome and Metabolome Reveals the Mechanism of Saline–Alkali Stress Tolerance in Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao

Saline–alkali stress is a major abiotic stress affecting the quality and yield of crops. Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus) is a well-known medicine food homology species with various pharmacological effects and health benefits that can grow well in saline–alkali soil. However, the molecular mechanisms underlying the adaptation of A. mongholicus plants to saline–alkali stress have not yet been clarified. Here, A. mongholicus plants were exposed to long-term saline–alkali stress (200 mmol·L -1 mixed saline–alkali solution), which limited the growth of A. mongholicus. The roots of A. mongholicus could resist long-term saline–alkali stress by increasing the activity of antioxidant enzymes and the content of osmolytes. Transcriptome analysis (via the Illumina platform) and metabolome analysis (via the Nexera UPLC Series QE Liquid Mass Coupling System) revealed that saline–alkali stress altered the activity of various metabolic pathways (e.g., amino acid metabolism, carbohydrate metabolism, lipid metabolism, and biosynthesis of other secondary metabolites). A total of 3,690 differentially expressed genes (DEGs) and 997 differentially accumulated metabolites (DAMs) were identified in A. mongholicus roots under saline–alkali stress, and flavonoid-related DEGs and DAMs were significantly up-regulated. Pearson correlation analysis revealed significant correlations between DEGs and DAMs related to flavonoid metabolism. MYB transcription factors might also contribute to the regulation of flavonoid biosynthesis. Overall, the results indicate that A. mongholicus plants adapt to saline–alkali stress by up-regulating the biosynthesis of flavonoids, which enhances the medicinal value of A. mongholicus.

Combined full-length transcriptomic and metabolomic analysis reveals the regulatory mechanisms of adaptation to salt stress in asparagus

Soil salinity is a very serious abiotic stressor that affects plant growth and threatens crop yield. Thus, it is important to explore the mechanisms of salt tolerance of plant and then to stabilize and improve crop yield. Asparagus is an important cash crop, but its salt tolerance mechanisms are largely unknown. Full-length transcriptomic and metabolomic analyses were performed on two asparagus genotypes: 'jx1502' (a salt-tolerant genotype) and 'gold crown' (a salt-sensitive genotype). Compared with the distilled water treatment (control), 877 and 1610 differentially expressed genes (DEGs) were identified in 'jx1502' and 'gold crown' under salt stress treatment, respectively, and 135 and 73 differentially accumulated metabolites (DAMs) were identified in 'jx1502' and 'gold crown' under salt stress treatment, respectively. DEGs related to ion transport, plant hormone response, and cell division and growth presented differential expression profiles between 'jx1502' and 'gold crown.' In 'jx1502,' 11 ion transport-related DEGs, 8 plant hormone response-related DEGs, and 12 cell division and growth-related DEGs were upregulated, while 7 ion transport-related DEGs, 4 plant hormone response-related DEGs, and 2 cell division and growth-related DEGs were downregulated. Interestingly, in 'gold crown,' 14 ion transport-related DEGs, 2 plant hormone response-related DEGs, and 6 cell division and growth-related DEGs were upregulated, while 45 ion transport-related DEGs, 13 plant hormone response-related DEGs, and 16 cell division and growth-related DEGs were downregulated. Genotype 'jx1502' can modulate K⁺/Na⁺ and water homeostasis and maintain a more constant transport system for nutrient uptake and distribution than 'gold crown' under salt stress. Genotype 'jx1502' strengthened the response to auxin (IAA), as well as cell division and growth for root remodeling and thus salt tolerance. Therefore, the integration analysis of transcriptomic and metabolomic indicated that 'jx1502' enhanced sugar and amino acid metabolism for energy supply and osmotic regulatory substance accumulation to meet the demands of protective mechanisms against salt stress. This work contributed to reveal the underlying salt tolerance mechanism of asparagus at transcription and metabolism level and proposed new directions for asparagus variety improvement.

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.

Comparative transcriptomic and metabolic profiling provides insight into the mechanism by which the autophagy inhibitor 3-MA enhances salt stress sensitivity in wheat seedlings

BACKGROUND

Salt stress hinders plant growth and production around the world. Autophagy induced by salt stress helps plants improve their adaptability to salt stress. However, the underlying mechanism behind this adaptability remains unclear. To obtain deeper insight into this phenomenon, combined metabolomics and transcriptomics analyses were used to explore the coexpression of differentially expressed-metabolite (DEM) and gene (DEG) between control and salt-stressed wheat roots and leaves in the presence or absence of the added autophagy inhibitor 3-methyladenine (3-MA).

RESULTS

The results indicated that 3-MA addition inhibited autophagy, increased ROS accumulation, damaged photosynthesis apparatus and impaired the tolerance of wheat seedlings to NaCl stress. A total of 14,759 DEGs and 554 DEMs in roots and leaves of wheat seedlings were induced by salt stress. DEGs were predominantly enriched in cellular amino acid catabolic process, response to external biotic stimulus, regulation of the response to salt stress, reactive oxygen species (ROS) biosynthetic process, regulation of response to osmotic stress, ect. The DEMs were mostly associated with amino acid metabolism, carbohydrate metabolism, phenylalanine metabolism, carbapenem biosynthesis, and pantothenate and CoA biosynthesis. Further analysis identified some critical genes (gene involved in the oxidative stress response, gene encoding transcription factor (TF) and gene involved in the synthesis of metabolite such as alanine, asparagine, aspartate, glutamate, glutamine, 4-aminobutyric acid, abscisic acid, jasmonic acid, ect.) that potentially participated in a complex regulatory network in the wheat response to NaCl stress. The expression of the upregulated DEGs and DEMs were higher, and the expression of the down-regulated DEGs and DEMs was lower in 3-MA-treated plants under NaCl treatment.

CONCLUSION

3-MA enhanced the salt stress sensitivity of wheat seedlings by inhibiting the activity of the roots and leaves, inhibiting autophagy in the roots and leaves, increasing the content of both H₂O₂ and O₂•-, damaged photosynthesis apparatus and changing the transcriptome and metabolome of salt-stressed wheat seedlings.

Pretreatment with H2O2 Alleviates the Negative Impacts of NaCl Stress on Seed Germination of Tartary Buckwheat (Fagopyrum tataricum)

Soil salinization is one of the main abiotic stress factors impacting the growth of crops and the agricultural industry today. Thus, we aimed to investigate the effects of H₂O₂ pretreatment on seed germination in Tartary buckwheat (Fagopyrum tataricum) seeds under salt stress and to evaluate this species’ salt tolerance. Through the preliminary experiment, this study used 50 mmol L⁻¹ NaCl solution to induce seed stress. After soaking for 12 h in different H₂O₂ concentrations, seeds were laid in Petri dishes with 50 mmol L⁻¹ NaCl for seven days and the germination parameters and physiological indicators were measured to screen the optimal H₂O₂ pretreatment concentration and the salt tolerance index. Our results indicated that pretreatment with 5–10 mmol L⁻¹ H₂O₂ was most effective in alleviating NaCl’s impacts on the seeds’ germination parameters. Furthermore, the growth and material accumulation of seedlings was promoted; catalase, superoxide dismutase activity, and proline content were enhanced; and malondialdehyde content was reduced. Principal component analysis and stepwise regression revealed six key indicators that had a significant impact on the salt tolerance characteristics of F. tataricum, namely, germination potential, shoot fresh weight, root surface area, root average diameter, catalase activity, and superoxide dismutase activity.

Metabolomics and health: from nutritional crops and plant-based pharmaceuticals to profiling of human biofluids

During the past decade metabolomics has emerged as one of the fastest developing branches of “-omics” technologies. Metabolomics involves documentation, identification, and quantification of metabolites through modern analytical platforms in various biological systems. Advanced analytical tools, such as gas chromatography–mass spectrometry (GC/MS), liquid chromatography–mass spectroscopy (LC/MS), and non-destructive nuclear magnetic resonance (NMR) spectroscopy, have facilitated metabolite profiling of complex biological matrices. Metabolomics, along with transcriptomics, has an influential role in discovering connections between genetic regulation, metabolite phenotyping and biomarkers identification. Comprehensive metabolite profiling allows integration of the summarized data towards manipulation of biosynthetic pathways, determination of nutritional quality markers, improvement in crop yield, selection of desired metabolites/genes, and their heritability in modern breeding. Along with that, metabolomics is invaluable in predicting the biological activity of medicinal plants, assisting the bioactivity-guided fractionation process and bioactive leads discovery, as well as serving as a tool for quality control and authentication of commercial plant-derived natural products. Metabolomic analysis of human biofluids is implemented in clinical practice to discriminate between physiological and pathological state in humans, to aid early disease biomarker discovery and predict individual response to drug therapy. Thus, metabolomics could be utilized to preserve human health by improving the nutritional quality of crops and accelerating plant-derived bioactive leads discovery through disease diagnostics, or through increasing the therapeutic efficacy of drugs via more personalized approach. Here, we attempt to explore the potential value of metabolite profiling comprising the above-mentioned applications of metabolomics in crop improvement, medicinal plants utilization, and, in the prognosis, diagnosis and management of complex diseases.

Proanthocyanidins and Where to Find Them: A Meta-Analytic Approach to Investigate Their Chemistry, Biosynthesis, Distribution, and Effect on Human Health

Proanthocyanidins (PACs) are a class of polyphenolic compounds that are attracting considerable interest in the nutraceutical field due to their potential health benefits. However, knowledge about the chemistry, biosynthesis, and distribution of PACs is limited. This review summarizes the main chemical characteristics and biosynthetic pathways and the main analytical methods aimed at their identification and quantification in raw plant matrices. Furthermore, meta-analytic approaches were used to identify the main plant sources in which PACs were contained and to investigate their potential effect on human health. In particular, a cluster analysis identified PACs in 35 different plant families and 60 different plant parts normally consumed in the human diet. On the other hand, a literature search, coupled with forest plot analyses, highlighted how PACs can be actively involved in both local and systemic effects. Finally, the potential mechanisms of action through which PACs may impact human health were investigated, focusing on their systemic hypoglycemic and lipid-lowering effects and their local anti-inflammatory actions on the intestinal epithelium. Overall, this review may be considered a complete report in which chemical, biosynthetic, ecological, and pharmacological aspects of PACs are discussed.

Distribution of polyphenolic and sugar compounds in different buckwheat plant parts

The aim of this study was to provide information on the phenolic and sugar profiles of different parts of the buckwheat plant, which can define that buckwheat is a functional food, with a high nutritional value and very useful for human health. Therefore, the extracts of buckwheat leaf, stem, and flower, as well as buckwheat grain were analysed for the content of polyphenol and antioxidant tests. The identification of a notable number of phenolic compounds and quantification of sugars in different parts of buckwheat indicates that buckwheat is a highly valuable plant. A total of 60 phenolic compounds were identified (18 cinnamic acid derivatives, 14 flavonols, 13 flavan-3-ols (including proanthocyanidins), 10 hydroxybenzoic acid derivatives, and 5 flavones) using ultra-high-performance liquid chromatography (UHPLC), coupled with a hybrid mass spectrometer which combines the Linear Trap Quadrupole (LTQ) and OrbiTrap mass analyzer. The highest number of phenolic compounds was found in the analysed buckwheat flower sample, and then in the leaf, followed by the grain and the stem. In addition, the sugar profile of buckwheat leaf, stem, flower and grain, as well as the buckwheat pollen and the nectar was analysed. Hence, 16 sugars and 5 sugar alcohols were detected by the high-performance anion exchange chromatography (HPAEC) with a pulsed amperometric detector (PAD). Sucrose was found in a significant amount with the highest content in buckwheat leaf. Trisaccharides had similar accumulation in the sample extracts, while disaccharides dominated in buckwheat leaf, followed by nectar and pollen. The sugar alcohols showed the highest content in buckwheat grain, where erythritol was predominant. The obtained results show that buckwheat is very rich in phenolic compounds and sugars. In addition to grain, the other parts of the buckwheat plant can be used as a very good source of different classes of phenolic compounds. This study provides useful information on the distribution of phytochemicals in different parts of the buckwheat plant, which contribute to the maintaining of the status of buckwheat as a functional food.

The aim of this study was to provide information on the phenolic and sugar profiles of different parts of the buckwheat plant, which can define that buckwheat is a functional food, with a high nutritional value and very useful for human health.

Elevated Ozone Levels Affect Metabolites and Related Biosynthetic Genes in Tartary Buckwheat

Global climate change and the industrial revolution have increased the concentration of tropospheric ozone, a photochemical air pollutant that can negatively affect plant growth and crop production. In the present study, we investigated the effects of O₃ on the metabolites and transcripts of tartary buckwheat. A total of 36 metabolites were identified by gas chromatography coupled with time-of-flight mass spectrometry, and principal component analysis was performed to verify the metabolic differences between nontreated and O₃-treated tartary buckwheat. The content of threonic acid increased after 2 days of the O₃ treatment, whereas it decreased after 4 days of exposure, after which it gradually increased until the eighth day of exposure. In addition, the levels of most metabolites decreased significantly after the O₃ treatment. On the contrary, the levels of two anthocyanins, cyanidin-3-O-glucoside and cyanidin-3-O-rutinoside, increased more than 11.36- and 11.43-fold, respectively, after the O₃ treatment. To assess the effect of O₃ on the genomic level, we analyzed the expression of anthocyanin biosynthesis pathway genes in O₃-treated and nontreated buckwheat using quantitative real-time reverse transcription polymerase chain reaction (PCR). We found that the expression of all anthocyanin pathway genes increased significantly in the O₃-treated buckwheat compared to that in the nontreated buckwheat. Altogether, our results suggested that O₃ affected the transcripts and metabolites of tartary buckwheat, which would eventually cause phenotypic changes in plants.

Transcriptomic and metabolomic analyses reveal mechanisms of adaptation to salinity in which carbon and nitrogen metabolism is altered in sugar beet roots

BACKGROUND

Beta vulgaris L. is one of the main sugar-producing crop species and is highly adaptable to saline soil. This study explored the alterations to the carbon and nitrogen metabolism mechanisms enabling the roots of sugar beet seedlings to adapt to salinity.

RESULTS

The ionome, metabolome, and transcriptome of the roots of sugar beet seedlings were evaluated after 1 day (short term) and 7 days (long term) of 300 mM Na+ treatment. Salt stress caused reactive oxygen species (ROS) damage and ion toxicity in the roots. Interestingly, under salt stress, the increase in the Na+/K+ ratio compared to the control ratio on day 7 was lower than that on day 1 in the roots. The transcriptomic results showed that a large number of differentially expressed genes (DEGs) were enriched in various metabolic pathways. A total of 1279 and 903 DEGs were identified on days 1 and 7, respectively, and were mapped mainly to 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the genes were involved in carbon metabolism and amino acid (AA) biosynthesis. Furthermore, metabolomic analysis revealed that sucrose metabolism and the activity of the tricarboxylic acid (TCA) cycle increased in response to salt stress. After 1 day of stress, the content of sucrose decreased, whereas the content of organic acids (OAs) such as L-malic acid and 2-oxoglutaric acid increased. After 7 days of salt stress, nitrogen-containing metabolites such as AAs, betaine, melatonin, and (S)-2-aminobutyric acid increased significantly. In addition, multiomic analysis revealed that the expression of the gene encoding xanthine dehydrogenase (XDH) was upregulated and that the expression of the gene encoding allantoinase (ALN) was significantly downregulated, resulting in a large accumulation of allantoin. Correlation analysis revealed that most genes were significantly related to only allantoin and xanthosine.

CONCLUSIONS

Our study demonstrated that carbon and nitrogen metabolism was altered in the roots of sugar beet plants under salt stress. Nitrogen metabolism plays a major role in the late stages of salt stress. Allantoin, which is involved in the purine metabolic pathway, may be a key regulator of sugar beet salt tolerance.