Study on metabolic variation in whole grains of four proso millet varieties reveals metabolites important for antioxidant properties and quality traits

Extensive targeted metabolomics analysis reveals the identification of major metabolites, antioxidants, and disease-resistant active pharmaceutical components in Camellia tuberculata (Camellia L.) seeds

Sect. tuberculata plant belongs to the Camellia genus and is named for the "tuberculiform protuberance on the surface of the ovary and fruit". It is a species of great ornamental value and potential medicinal value. However, little has been reported on the metabolites of C. tuberculata seeds. Therefore, this study was conducted to investigate the metabolites of C. tuberculata seeds based on UPLC/ESI-Q TRAP-MS/MS with extensively targeted metabolomics. A total of 1611 metabolites were identified, including 107 alkaloids, 276 amino acids and derivatives, 283 flavonoids, 86 lignans and coumarins, 181 lipids, 68 nucleotides and derivatives, 101 organic acids, 190 phenolic acids, 10 quinones, 4 steroids, 17 tannins, 111 terpenoids, and 177 other metabolites. We compared the different metabolites in seeds between HKH, ZM, ZY, and LY. The 1311 identified different metabolites were classified into three categories. Sixty-three overlapping significant different metabolites were found, of which lignans and coumarins accounted for the largest proportion. The differentially accumulated metabolites were enriched in different metabolic pathways between HKH vs. LY, HKH vs. ZM, HKH vs. ZY, LY vs. ZY, ZM vs. LY and ZM vs. ZY, with the most abundant metabolic pathways being 4, 2, 4, 7, 7 and 5, respectively (p < 0.05). Moreover, among the top 20 metabolites in each subgroup comparison in terms of difference multiplicity 7, 8 and 13. ZM and ZY had the highest phenolic acid content. Ninety-six disease-resistant metabolites and 48 major traditional Chinese medicine agents were identified based on seven diseases. The results of this study will not only lead to a more comprehensive and in-depth understanding of the metabolic properties of C. tuberculata seeds, but also provide a scientific basis for the excavation and further development of its medicinal value.

Widely Targeted Metabolomics Analysis Reveals Metabolites Important for Antioxidant Properties and Quality Traits in Different Fruit Parts of Aurantii Fructus Immatures

In traditional Chinese medicine, Aurantii Fructus Immatures (AFIs) have been utilized for more than 2000 years. The proportions of different fruit parts are crucial for evaluating AFI quality in China. However, the basis for this statement's substance is unclear. Differences in quality are intimately correlated with a plant's metabolite composition. On the basis of a widely targeted metabolome, this study intended to investigate the metabolite composition and evaluate the antioxidant capacity of the peel and pulp of an AFI. Metabolites were identified and quantified by UHPLC-QqQ-MS. To assess their antioxidant ability, DPPH and ABTS assays were carried out. There were 1327 chemical compounds identified by UHPLC-QqQ-MS. After screening the differential metabolites using a multivariate statistical analysis, it was found that there were 695 significant differences in the metabolites between the peel and the pulp. Among them, it was discovered that the content of active ingredients in the peel group was higher than that in the pulp group. Furthermore, the aqueous extracts from the peel showed stronger antioxidant capacities than those from the pulp. The metabolites and antioxidant capacities were significantly different between the peel and the pulp. This study of different fruit parts might provide a guide for AFI quality assessments.

Widely targeted metabolomics-based analysis of the impact of L. plantarum and L. paracasei fermentation on rosa roxburghii Tratt juice

Rosa roxburghii Tratt fruits (RRT) exhibit extremely high nutritional and medicinal properties due to its unique phytochemical composition. Probiotic fermentation is a common method of processing fruits. Variations in the non-volatile metabolites and bioactivities of RRT juice caused by different lactobacilli are not well understood. Therefore, we aimed to profile the non-volatile components and investigate the impact of L. plantarum fermentation (LP) and L. paracasei fermentation (LC) on RRT juice (the control, CG). There were both similarities and differences in the effects of LP and LC on RRT juice. Both of the two strains significantly increased the content of total phenolic, total flavonoid, and some bioactive compounds such as 2-hydroxyisocaproic acid, hydroxytyrosol and indole-3-lactic acid in RRT juice. Interestingly, compared with L. paracasei, L. plantarum showed better ability to increase the content of total phenolic and these valuable compounds, as well as certain bioactivities. The antioxidant capacity and α-glucosidase inhibitory activity of RRT juice were notably enhanced after the fermentations, whereas its cholesterol esterase inhibitory activity was reduced significantly. Moreover, a total of 1466 metabolites were identified in the unfermented and fermented RRT juices. There were 278, 251 and 134 differential metabolites in LP vs CG, LC vs CG, LC vs LP, respectively, most of which were upregulated. The key differential metabolites were classified into amino acids and their derivatives, organic acids, nucleotides and their analogues, phenolic acids and alkaloids, which can serve as potential markers for authentication and discrimination between the unfermented and lactobacilli fermented RRT juice samples. The KEGG enrichment analysis uncovered that metabolic pathways, purine metabolism, nucleotide metabolism and ABC transporters contributed mainly to the formation of unique composition of fermented RRT juice. These results provide good coverage of the metabolome of RRT juice in both unfermented and fermented forms and also provide a reference for future research on the processing of RRT or other fruits.

Dictyophora indusiata and Bacillus aryabhattai improve sugarcane yield by endogenously associating with the root and regulating flavonoid metabolism

Introduction

Endophytes play a significant role in regulating plant root development and facilitating nutrient solubilization and transportation. This association could improve plant growth. The present study has uncovered a distinct phenotype, which we refer to as "white root", arising from the intricate interactions between endophytic fungi and bacteria with the roots in a sugarcane and bamboo fungus (Dictyophora indusiata) intercropping system.

Methods

We investigated the mechanisms underlying the formation of this "white root" phenotype and its impact on sugarcane yield and metabolism by metabarcoding and metabolome analysis.

Results and Discussion

Initial analysis revealed that intercropping with D. indusiata increased sugarcane yield by enhancing the number of viable tillers compared with bagasse and no input control. Metabarcoding based on second-generation and third-generation sequencing indicated that D. indusiate and Bacillus aryabhattai dominates the fungal and bacterial composition in the "white root" phenotype of sugarcane root. The coexistence of D. indusiata and B. aryabhattai as endophytes induced plant growth-promoting metabolites in the sugarcane root system, such as lysoPC 18:1 and dihydrobenzofuran, probably contributing to increased sugarcane yield. Furthermore, the association also enhanced the metabolism of compounds, such as naringenin-7-O-glucoside (Prunin), naringenin-7-O-neohesperidoside (Naringin)*, hesperetin-7-O-neohesperidoside (Neohesperidin), epicatechin, and aromadendrin (Dihydrokaempferol), involved in flavonoid metabolism during the formation of the endophytic phenotype in the sugarcane root system. These observations suggest that the "white root" phenotype promotes sugarcane growth by activating flavonoid metabolism. This study reports an interesting phenomenon where D. indusiata, coordinate with the specific bacteria invade, forms a "white root" phenotype with sugarcane root. The study also provides new insights into using D. indusiata as a soil inoculant for promoting sugarcane growth and proposes a new approach for improve sugarcane cultivation.

An investigation into the effects of various processing methods on the characteristic compounds of highland barley using a widely targeted metabolomics approach

This study explored the influence of diverse processing methods (cooking (CO), extrusion puffing (EX), and steam explosion puffing (SE), stir-frying (SF) and fermentation (FE)) on highland barley (Qingke) chemical composition using UHPLC-MS/MS based widely targeted metabolomics. Overall, 827 metabolites were identified and categorized into 16 classes, encompassing secondary metabolites, amino acids, nucleotides, lipids, etc. There 43, 85, 131, 51 and 98 differential metabolites were respectively selected from five comparative groups (raw materials (RM) vs CO/EX/SE/SF/FE), mainly involved in amino acids, nucleotides, flavonoids, and alkaloids. Compared to other treated groups, FE group possessed the higher content of crude protein (15.12 g/100 g DW), and the relative levels of free amino acids (1.32 %), key polyphenols and arachidonic acid (0.01 %). EX group had the higher content of anthocyanins (4.22 mg/100 g DW), and the relative levels of free amino acids (2.02 %) and key polyphenols. SE group showed the higher relative levels of phenolic acids (0.14 %), flavonoids (0.20 %) and alkaloids (1.17 %), but the lowest free amino acids (0.75 %). Different processing methods all decreased Qingke's antioxidant capacity, with the iron reduction capacity (988.93 μmol/100 g DW) in SE group was the lowest. On the whole, FE and EX were alleged in improving Qingke's nutritional value. CO and SF were also suitable for Qingke processing since fewer differential metabolites were identified in CO vs RM and SF vs RM groups. Differential metabolites were connected to 14 metabolic pathways, with alanine, aspartate, and glutamate metabolism being central. This study contributed theoretical groundwork for the scientific processing and quality control of Qingke products.

Cytokinin promotes anthocyanin biosynthesis via regulating sugar accumulation and MYB113 expression in Eucalyptus

Anthocyanins are flavonoid-like substances that play important roles in plants' adaptation to various environmental stresses. In this research, we discovered that cytokinin (CK) alone could effectively induce the anthocyanin biosynthesis in Eucalyptus and many other perennial woody plant species, but not in tobacco and Arabidopsis, suggesting a diverse role of CK in regulating anthocyanin biosynthesis in different species. Transcriptomic and metabolomic strategies were used to further clarify the specific role of CK in regulating anthocyanin biosynthesis in Eucalyptus. The results showed that 801 and 2241 genes were differentially regulated at 6 and 24 h, respectively, after CK treatment. Pathway analysis showed that most of the differentially expressed genes were categorized into pathways related to cellular metabolism or transport of metabolites, including amino acids and sugars. The metabolomic results well supported the transcriptome data, which showed that most of the differentially regulated metabolites were related to the metabolism of sugar, amino acids and flavonoids. Moreover, CK treatment significantly induced the accumulation of sucrose in the CK-treated leaves, while sugar starvation mimicked by either defoliation or shading treatment of the basal leaves significantly reduced the sugar increase of the CK-treated leaves and thus inhibited CK-induced anthocyanin biosynthesis. The results of in vitro experiment also suggested that CK-induced anthocyanin in Eucalyptus was sugar-dependent. Furthermore, we identified an early CK-responsive transcription factor MYB113 in Eucalyptus, the expression of which was significantly upregulated by CK treatment in Eucalyptus, but was inhibited in Arabidopsis. Importantly, the overexpression of EgrMYB113 in the Eucalyptus hairy roots was associated with significant anthocyanin accumulation and upregulation of most of the anthocyanin biosynthetic genes. In conclusion, our study demonstrates a key role of CK in the regulation of anthocyanin biosynthesis in Eucalyptus, providing a molecular basis for further understanding the regulatory mechanism and diversity of hormone-regulated anthocyanin biosynthesis in different plant species.

Integrated Metabolomic and Transcriptomic Analysis of Puerarin Biosynthesis in Pueraria montana var. thomsonii at Different Growth Stages

Puerarin, a class of isoflavonoid compounds concentrated in the roots of Puerarias, has antipyretic, sedative, and coronary blood-flow-increasing properties. Although the biosynthetic pathways of puerarin have been investigated by previous researchers, studies focusing on the influence of different growth stages on the accumulation of metabolites in the puerarin pathway are not detailed, and it is still controversial at the last step of the 8-C-glycosylation reaction. In this study, we conducted a comprehensive analysis of the metabolomic and transcriptomic changes in Pueraria montana var. thomsonii during two growing years, focusing on the vigorous growth and dormant stages, to elucidate the underlying mechanisms governing the changes in metabolite and gene expression within the puerarin biosynthesis pathway. In a comparison of the two growth stages in the two groups, puerarin and daidzin, the main downstream metabolites in the puerarin biosynthesis pathway, were found to accumulate mainly during the vigorous growth stage. We also identified 67 common differentially expressed genes in this pathway based on gene expression differences at different growth stages. Furthermore, we identified four candidate 8-C-GT genes that potentially contribute to the conversion of daidzein into puerarin and eight candidate 7-O-GT genes that may be involved in the conversion of daidzein into daidzin. A co-expression network analysis of important UGTs and HIDs along with daidzein and puerarin was conducted. Overall, our study contributes to the knowledge of puerarin biosynthesis and offers information about the stage at which the 8-C-glycosylation reaction occurs in biosynthesis. These findings provide valuable insights into the cultivation and quality enhancement of Pueraria montana var. thomsonii.

A comparative metabolomics study of polyphenols in highland barley (Hordeum vulgare L.) grains with different colors

Highland barley (HB) grains are gaining increasing popularity owing to their high nutritional merits. However, only limited information is available on the metabolic profiles of HB grains polyphenols, especially the difference of polyphenols in different colors of HB. In this study, we determined the metabolic profiles of black, blue, and white HB grains via an ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based metabolomics. A total of 402 metabolites were identified, among which 198, 62, and 189 metabolites displayed different accumulation patterns in the three comparison groups (WHB vs. BKHB, WHB vs. BEHB, BEHB vs. BKHB), respectively. In particular, flavonoids and phenolic acids contents displayed considerable differences among the three HB cultivars. The phenolics content of black HB was relatively high. Additionally, "Flavonoid biosynthesis" and "flavone and flavonol biosynthesis" were the significantly enriched pathways. In conclusion, this study provides comprehensive insights into the adequate utilization and development of novel HB-based functional foods.

Effect of lactic acid bacteria co-fermentation on antioxidant activity and metabolomic profiles of a juice made from wolfberry and longan

Lactic acid bacteria (LAB) fermentation is frequently employed to improve the nutritional, functional, and sensory characteristics of foods. Our study explored the effects of co-fermentation with Lacticaseibacillus paracasei ZH8 and Lactococcus lactis subsp. lactis YM313 on the physicochemical properties, antioxidant activity, and metabolomic profiles of wolfberry-longan juice (WLJ). Fermentation was carried out at 35 °C for 15 h. The results suggest that WLJ is a favorable substrate for LAB growth, reaching a total viable count exceeding 8 log CFU/mL after fermentation. LAB fermentation increased acidity, reduced the sugar content, and significantly impacted the juice color. The total phenolic and flavonoid contents of the WLJ and the antioxidant capacities based on 2,2-diphenyl-1-picrylhydrazyl (DPPH), ABTS radical scavenging abilities and FRAP were significantly improved by LAB fermentation. Nontargeted metabolomics analysis suggested that the contents of small molecule substances in WLJ were considerably affected by LAB fermentation. A total of 374 differential metabolites were identified in the juice before and after fermentation, with 193 significantly upregulated metabolites and 181 siginificantly downregulated metabolites. The regulation of metabolites is important for improving the flavor and functions of juices, such as L-eucylproline, Isovitexin, Netivudine, 3-Phenyllactic acid, vanillin, and ethyl maltol, ect. This study provides a theoretical foundation for developing plant-based foods fermented with LAB.

Integrated metabolomics and network pharmacology to reveal antioxidant mechanisms and potential pharmacological ingredients of citrus herbs

The benefits of citrus herbs are strongly associated with their secondary metabolites. In the study, we conducted widely-targeted metabolomics and ultra-high performance liquid chromatography (UPLC) to compare the variability of ingredients in four citrus herbs. In total, we discovered 1126 secondary metabolites, primarily comprising flavonoids, phenolic acids, lignans and coumarins, and alkaloids. Differential metabolites of citrus herbs were searched by multivariate statistical analysis. Notably, Citri Reticulatae Pericarpium contained higher levels of flavonoids, while Zhique and Huajuhong demonstrated a greater abundance of coumarins. Among the flavonoids determined by UPLC, Guangchenpi demonstrated significantly elevated levels of polymethoxyflavones (tangeretin and nobiletin) compared to other citrus herbs. Additionally, we determined their antioxidant capacity (Chenpi > Guangchenpi > Huajuhong > Zhique) using in vitro assays. Finally, we utilized network pharmacology to explore the antioxidant mechanisms and potential pharmacological ingredients, providing a basis for future preventive and therapeutic applications of these metabolites.

Comparative analysis of flavonoid metabolites from different parts of Hemerocallis citrina

BACKGROUND

Hemerocallis citrina Baroni is a traditional medical and edible plant. It is rich in flavonoid compounds, which are a kind of important bioactive components with various health benefits and pharmaceutical value. However, the flavonoid metabolomics profile and the comparison of flavonoid compounds from different parts of H. citrina is scarce.

RESULTS

In this study, flavonoid metabolites were investigated from roots, stems, leaves and flowers of H. citrina. A total of 364 flavonoid metabolites were identified by UPLC-MS/MS based widely targeted metabolomics, and the four plant parts showed huge differences at flavonoid metabolic level. Compared to roots, 185, 234, and 119 metabolites accounted for upregulated differential flavonoid metabolites (DFMs) in stems, leaves, and flowers, respectively. Compared to stems, 168 and 29 flavonoid metabolites accounted for upregulated DFMs in leaves and flowers, respectively. Compared to leaves, only 29 flavonoid metabolites accounted for upregulated DFMs in flowers. A number of 35 common flavonoid metabolites were observed among six comparison groups, and each comparison group had its unique differential metabolites. The most abundant flavonoid metabolites in the four parts are flavonols and flavones, followed by flavanones, chalcones, flavanols, flavanonols, anthocyanidins, tannin, and proanthocyanidins. 6,7,8-Tetrahydroxy-5-methoxyflavone, 7,8,3',4'-tetrahydroxyflavone, 1-Hydroxy-2,3,8-trimethoxyxanthone, Farrerol-7-O-glucoside, 3',7-dihydroxy-4'-methoxyflavone, 3,3'-O-Dimethylellagic Acid, 5-Hydroxy-6,7-dimethoxyflavone, Nepetin (5,7,3',4'-Tetrahydroxy-6-methoxyflavone), (2s)-4,8,10-trihydroxy-2-methoxy-1 h,2 h-furo[3,2-a]xanthen-11-one are dominant in roots. Isorhamnetin-3-O-(6''-malonyl)glucoside-7-O-rhamnoside, 7-Benzyloxy-5-hydroxy-3',4'-methylenedioxyflavonoid, 3-Hydroxyphloretin-4'-O-glucoside are dominant in stems. Chrysoeriol-7-O-glucoside, Epicatechin glucoside, Kaempferol-3-O-rhamnoside (Afzelin)(Kaempferin)*, Azaleatin (5-O-Methylquercetin), Chrysoeriol-5-O-glucoside, Nepetin-7-O-glucoside(Nepitrin), 3,5,7,2'-Tetrahydroxyflavone; Datiscetin, Procyanidin B2*, Procyanidin B3*, Procyanidin B1, Isorhamnetin-3-O-(6''-acetylglucoside) are dominant in leaves. kaempferol-3-p-coumaroyldiglucoside, Delphinidin-3-O-sophoroside-5-O-glucoside, Limocitrin-3-O-sophoroside, Kaempferol-3-O-rutinoside(Nicotiflorin), Luteolin-7-O-(6''-malonyl)glucoside-5-O-rhamnoside are dominant in flowers.

CONCLUSION

There was significant difference in flavonoid metabolites among different parts of H. citrina. Leaves had relative higher metabolites contents than other parts. This study provided biological and chemical evidence for the different uses of various plant parts of H. citrina, and these informations are important theoretical basis for the food industry, and medical treatment.

Study on the metabolic process of phthalic acid driven proliferation of Rhizoctonia solani

Introduction

Continuous cropping obstacle seriously affects the quality and yield of Salvia miltiorrhiza, and the synergistic effect of root exudates and rhizosphere pathogenic microorganisms may be an important cause of continuous cropping obstacle. This study aimed to explore the effects of representative organic acids on the growth and metabolism of specific microorganisms in the S. miltiorrhiza rhizosphere soil under continuous cropping, and clarify its mechanism.

Methods

The effect of phthalic acid (PA) on the growth and metabolism of Rhizoctonia solani was evaluated by mycelial growth inhibition method. Ultra-high performance liquid chromatography and tandem mass spectrometry were used to identify the differential metabolites of R. solani induced by exogenous PA.

Results

PA exerted a concentration-dependent effect on mycelial growth, biomass, intracellular polysaccharides con-tent, and total protein content in R. solani. A total of 1773 metabolites and 1040 differential metabolites were identified in the blank medium (CK), Fungi (CK + fungi), and PA-Fungi (CK + fungi + acid) groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the differential metabolites were mainly involved in the sugar, lipid, and protein metabolic pathways related to stable membrane structure and cell growth.

Discussion

The proliferation and metabolism network of R. solani induced by PA was proposed, and the enhancement of sugar, lipid, and amino acid metabolism was presumed to be related to the active resistance of cells to organic acid stress. These results offer new in-sights into the effects of PA metabolism on promoting R. solani proliferation, and provide theoretical support for further optimizing the rhizosphere microecological environment of Salvia miltiorrhiza continuous cropping soil and reducing continuous cropping obstacle.

Study on the material basis and mechanism of Hemerocallis citrina Baroni on sleep-improvement using Drosophila activity monitoring, metabolomic, targeted screening and transcriptomic

Daylily (Hemerocallis citrina Baroni, HC) is an edible plant and is traditionally considered with potential to improve sleep. Herein, based on the Drosophila activity monitoring, metabolome, targeted screening and transcriptome, the material basis and mechanism of HC on sleep-improvement was investigated. The results showed that the aqueous extracts of HC (HAE) as well as the ethanol extracts (HEE) all prolonged the total sleep time of insomnia fruit flies, especially HEE-60 and HEE-95 exhibited more significant effects. In addition, 539 of 728 found metabolites were screened as potential sleep-improved metabolites, and quercetin, linoleic acid, phenethyl caffeate, L-methionine and γ-aminobutyric acid were considered as core active metabolites. Meanwhile, 368 differentially expressed genes (DEGs) were revealed by transcriptomics analysis, and the neuroactive ligand-receptor interaction was deduced as the main pathway by KEGG pathway enrichment. Furthermore, nine DEGs located in this pathway, namely betaTry, deltaTry, gammaTry, epsilonTry, etaTry, iotaTry, lambdaTry, kappaTry and CG30031 were proven being up-regulated. All these results contribute to the development of HC-related functional foods.

Metabolic responses of tea (Camellia sinensis L.) to the insecticide thiamethoxam

BACKGROUND

Thiamethoxam (TMX) is insecticidal, but also can trigger physiological and metabolic reactions of plant cycles. The objective of this work was to evaluate the physiological and metabolic effect of TMX on tea plants and its potential benefits.

RESULTS

In this study, dose of TMX (0.09, 0.135 and 0.18 kg a.i./ha) were tested. Except for peroxidase (POD) and glutathione S-transferase (GST), chlorophyll, carotenoid, catalase (CAT) and malondialdehyde (MDA) were significantly affected compared with the controls. The CAT activity was increased by 3.38, 1.71, 2.91 times, respectively, under three doses of TMX treatment. The metabolic response between TMX treatment and control groups on the third day was compared using a widely targeted metabolomics. A total of 97 different metabolites were identified, including benzenoids, flavonoids, lipids and lipid-like molecules, organic acids and derivatives, organic nitrogen compounds, organic oxygen compounds, organoheterocyclic compounds, phenylpropanoids and polyketides, and others. Those metabolites were mapped on the perturbed metabolic pathways. The results demonstrated that the most perturbation occurred in flavone and flavonol biosynthesis. The beneficial secondary metabolites luteolin and kaempferol were upregulated 1.46 and 1.31 times respectively, which protect plants from biotic and abiotic stresses. Molecular docking models suggest interactions between TMX and flavonoid 3-O-glucosyltransferase.

CONCLUSION

Thiamethoxam spray positively promoted the physiological and metabolic response of tea plants. And this work also provided the useful information of TMX metabolism in tea plants as well as rational application of insecticides. © 2023 Society of Chemical Industry.

Uncovering the differences in flavor volatiles of different colored foxtail millets based on gas chromatography-ion migration spectrometry and chemometrics

The differences of volatile organic compounds in commercially available foxtail millets with different colors (black, green, white and yellow) were assayed through gas chromatography-ion migration spectrometry (GC-IMS) to explore their volatile flavor characteristics. Fifty-five volatile components were found in various colored foxtail millets, including 25 kinds of aldehydes (accounting for 39.19-48.69%), 10 ketones (25.36-32.37%), 15 alcohols (20.19-24.11%), 2 ethers (2.29-2.45%), 2 furans (1.49-2.95%) and 1 ester (0.27-0.39%). Aldehydes, alcohols and ketones were the chief volatiles in different colored foxtail millet, followed by furans, esters and ethers. These identified volatile flavor components in various colored foxtail millets obtained by GC-IMS could be well distinguished by principal components and cluster analysis. Meanwhile, a stable prediction model was fitted via partial least squares-discriminant analysis (PLS-DA), in which 17 kinds of differentially volatile components were screened out based on variable importance in projection (VIP>1). These findings might provide certain information for understanding the flavor traits of colored foxtail millets in future.

Widely targeted metabolomic analysis revealed the effects of alkaline stress on nonvolatile and volatile metabolites in broomcorn millet grains

Broomcorn millet (BM) is a future smart food. However, no information is available on the metabolism of BM grains under alkaline stress. In this study, the effects of alkaline stress on nonvolatile and volatile metabolites in the BM grains of two varieties (S223 and T289) were investigated through metabolomics approaches. All 933 nonvolatile metabolites and 313 volatile metabolites were identified, with 114 and 89 nonvolatile metabolites and 16 and 20 volatile metabolites accumulating differentially under normal vs. alkaline stresses of S223 and T289, respectively. The results indicated that alkaline stress altered phenylpropanoids, flavonoids, flavone and flavonol, valine, leucine, and isoleucine biosynthesis, as well as arginine, proline, tryptophan, and ascorbate metabolism. The effects of alkaline stress were not identical between the two varieties, which could lead to variations in active substance content. These results provide valuable information for further studies on food chemistry and the functional food development of BM grains.

Integrated Metabolome and Transcriptome Analyses Reveal Amino Acid Biosynthesis Mechanisms during the Physiological Maturity of Grains in Yunnan Hulled Wheat (Triticum aestivum ssp. yunnanense King)

Yunnan hulled wheat (YHW) possesses excellent nutritional characteristics; however, the precise amino acid (AA) composition, contents, and molecular mechanisms underlying AA biosynthesis in YHW grains remain unclear. In this study, we aimed to perform metabolomic and transcriptomic profiling to identify the composition and genetic factors regulating AA biosynthesis during the physiological maturation of grains of two YHW genotypes, Yunmai and Dikemail, with high and low grain protein contents, respectively. A total of 40 and 14 differentially accumulated amino acids (AAs) or AA derivatives were identified between the waxy grain (WG) and mature grain (MG) phenological stages of Yunmai and Dikemail, respectively. The AA composition differed between WG and MG, and the abundance of AAs-especially that of essential AAs-was significantly higher in WG than in MG (only 38.74-58.26% of WG). Transcriptome analysis revealed differential regulation of structural genes associated with the relatively higher accumulation of AAs in WG. Weighted gene co-expression network analysis and correlation analyses of WG and MG indicated differences in the expression of clusters of genes encoding both upstream elements of AA biosynthesis and enzymes that are directly involved in AA synthesis. The expression of these genes directly impacted the synthesis of various AAs. Together, these results contribute to our understanding of the mechanism of AA biosynthesis during the different developmental stages of grains and provide a foundation for further research to improve the nutritional value of wheat products.

Proso Millet (Panicum miliaceum L.) as Alternative Source of Starch and Phenolic Compounds: A Study on Twenty-Five Worldwide Accessions

Proso millet has been proposed as an effective anti-diabetic food thanks to the combined action of polyphenols and starch. This study aimed to characterize the chemical composition of twenty-five accessions, in order to enhance this cereal as an alternative to available starch for food applications or to propose new food ingredients with health benefits. Proso millet contained a high percentage of starch, reaching values of 58.51%. The amylose content showed high variability, with values ranging from 1.36 to 42.70%, and significantly higher values were recorded for the white accessions than for the colored ones. High-resistant starch content (13.41-26.07%) was also found. The HPLC-MS analysis showed the same phenolic pattern in all the samples. Cinnamic acids are the most abundant compounds and significant differences in their total content were found (0.69 to 1.35 mg/g DW), while flavonoids were only detected in trace amounts. Statistical results showed significantly higher antiradical activity in the colored accessions than in the white ones.

Modification on phenolic profiles and enhancement of antioxidant activity of proso millets during germination

Changes in phenolic profiles and antioxidant activity of three varieties of proso millet during germination were investigated. Total phenolic content (TPC) and total flavonoid content (TFC) increased significantly with prolongation in germination period. After germination for 6 days, TPC of the free and bound fractions increased 6.30-8.66-fold and 77.65-116.18%, respectively. The free and bound phenolic compounds identified by UPLC-MS/MS, displayed significant variations. Feruloylquinic acid and N,N'-bis-(p-coumaroyl)-putrescine biosynthesized during germination, are reported for the first time in proso millets. Other phenolics including trans- and cis-ferulic, trans-p-coumaric, vanillic acid and ferulic acid dimers (DFAs) were increased significantly along with a new DFA (8,5'-DFA) seemingly produced during germination. The germinated proso milllets displayed superior antioxidant activity than the corresponding ungerminated samples indicating that germination could be one applicable method for improving phenolic profiles and antioxidant capacity of proso millets. Thus germinated proso millet could be exploited as a functional ingredient in several products.

Development of a Comprehensive Quality Evaluation System for Foxtail Millet from Different Ecological Regions

Foxtail millet (Setaria italica L.) is a critical grain with high nutritional value and the potential for increased production in arid and semiarid regions. The foxtail millet value chain can be upgraded only by ensuring its comprehensive quality. Thus, samples were collected from different production areas in Shanxi province, China, and compared in terms of quality traits. We established a quality evaluation system utilizing multivariate statistical analysis. The results showed that the appearance, nutritional content, and culinary value of foxtail millet produced in different ecological regions varied substantially. Different values of amino acids (DVAACs), alkali digestion values (ADVs), and total flavone content (TFC) had the highest coefficients of variation (CVs) of 50.30%, 39.75%, and 35.39%, respectively. Based on this, a comprehensive quality evaluation system for foxtail millet was established, and the quality of foxtail millet produced in the five production areas was ranked in order from highest to lowest: Dingxiang > Zezhou > Qinxian > Xingxian > Yuci. In conclusion, the ecological conditions of Xinding Basin are favorable for ensuring the comprehensive quality of foxtail millet. .

The potentialities of omics resources for millet improvement

Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.

The Role of Ancient Grains in Alleviating Hunger and Malnutrition

Meeting the United Nation's sustainable development goals for zero hunger becomes increasingly challenging with respect to climate change and political and economic challenges. An effective strategy to alleviate hunger and its severe implications is to produce affordable, nutrient-dense, and sustainable food products. Ancient grains were long-forgotten due to the dominance of modern grains, but recently, they have been rediscovered as highly nutritious, healthy and resilient grains for solving the nutrition demand and food supply chain problems. This review article aims to critically examine the progress in this emerging field and discusses the potential roles of ancient grains in the fight against hunger. We provide a comparative analysis of different ancient grains with their modern varieties in terms of their physicochemical properties, nutritional profiles, health benefits and sustainability. A future perspective is then introduced to highlight the existing challenges of using ancient grains to help eradicate world hunger. This review is expected to guide decision-makers across different disciplines, such as food, nutrition and agronomy, and policymakers in taking sustainable actions against malnutrition and hunger.

Analysis of the utilization value of different tissues of Taxus×Media based on metabolomics and antioxidant activity

BACKGROUND

Taxaceae, is a class of dioecious and evergreen plant with substantial economic and ecology value. At present many phytochemical analyses have been performed in Taxus plants. And various biological constituents have been isolated from various Taxus species. However, the difference of compounds and antioxidant capacity of different tissues of T. media is not clear.

RESULTS

In the present study, we investigated the metabolites and antioxidant activity of four tissues of T. media, including T. media bark (TB), T. media fresh leaves (TFL), T. media seeds (TS), T. media aril (TA). In total, 808 compounds, covering 11 subclasses, were identified by using UPLC-MS/MS. Paclitaxel, the most popular anticancer compound, was found to accumulate most in TS, followed by TB, TFL and TA in order. Further analysis found that 70 key differential metabolites with VIP > 1.0 and p < 0.05, covering 8 subclasses, were screened as the key differential metabolites in four tissues. The characteristic compounds of TFL mainly included flavonoids and tanninsis. Alkaloids and phenolic acids were major characteristic compounds of TS and TB respectively. Amino acids and derivatives, organic acids, saccharides and lipids were the major characteristic compounds of TA. Additionally, based on FRAP and ABTS method, TS and TFL exhibited higher antioxidant activity than TB and TA.

CONCLUSION

There was significant difference in metabolite content among different tissues of T. media. TFL and TS had higher metabolites and antioxidant capacity than other tissues, indicating that TFL and TS were more suitable for the development and utilization of T. media in foods and drinks.

Widely targeted metabolome profiling of different plateau raspberries and berry parts provides innovative insight into their antioxidant activities

Raspberries are highly nutritious and have powerful antioxidant properties, making them functional berries with positive effects on physiological functioning. However, there is limited information available on the diversity and variability of metabolites in raspberry and its parts, especially in plateau raspberries. To address this, commercial raspberries and their pulp and seeds from two plateaus in China were subjected to LC-MS/MS-based metabolomics analysis and evaluated for antioxidant activity using four assays. A metabolite-metabolite correlation network was established based on antioxidant activity and correlation analysis. The results showed that 1661 metabolites were identified and classified into 12 categories, with significant variations in composition between the whole berry and its parts from different plateaus. Flavonoids, amino acids and their derivatives, and phenolic acids were found to be up-regulated in Qinghai's raspberry compared to Yunnan's raspberry. The main differently regulated pathways were related to flavonoid, amino acid, and anthocyanin biosynthesis. The antioxidant activity of Qinghai's raspberry was stronger than Yunnan's raspberry, and the order of antioxidant capacity was seed > pulp > berry. The highest FRAP (420.31 µM TE/g DW) values was found in the seed of Qinghai's raspberry. Overall, these findings suggest that the environment in which the berries grow can affect their chemical composition, and comprehensive exploitation and cultivation of whole raspberry and its parts from different plateaus can lead to new opportunities for phytochemical compositions and antioxidant activity.

Genome, transcriptome, and metabolome analyses provide new insights into the resource development in an edible fungus Dictyophora indusiata

Dictyophora indusiata (Vent. Ex Pers.) Fisch. (DI) is an edible and medicinal fungus widely used in East Asian countries. However, during DI cultivation, the formation of fruiting bodies cannot be regulated, which leads to yield and quality losses. The present study performed a combined genome, transcriptome, and metabolome analysis of DI. Using Nanopore and Illumina sequencing approaches, we created the DI reference genome, which was 67.32 Mb long with 323 contigs. We identified 19,909 coding genes on this genome, of which 46 gene clusters were related to terpenoid synthesis. Subsequent transcriptome sequencing using five DI tissues (cap, indusia, mycelia, stipe, and volva) showed high expression levels of genes in the cap, indicating the tissue's importance in regulating the fruiting body formation. Meanwhile, the metabolome analysis identified 728 metabolites from the five tissues. Mycelium was rich in choline, while volva was rich in dendronobilin; stipe had monosaccharides as the primary component, and the cap was the main source of indole acetic acid (IAA) synthesis. We confirmed the importance of tryptophan metabolism for DI fruiting body differentiation based on KEGG pathway analysis. Finally, the combined multiomics analysis identified three new genes related to IAA synthesis of the tryptophan metabolic pathway in the cap, which may regulate DI fruiting body synthesis and improve DI quality. Thus, the study's findings expand our understanding of resource development and the molecular mechanisms underlying DI development and differentiation. However, the current genome is still a rough draft that needs to be strengthened.

Drying sea buckthorn berries (Hippophae rhamnoides L.): Effects of different drying methods on drying kinetics, physicochemical properties, and microstructure

Sea buckthorn berries are important ingredients in Chinese medicine and food processing; however, their high moisture content can reduce their shelf life. Effective drying is crucial for extending their shelf life. In the present study, we investigated the effects of hot-air drying (HAD), infrared drying (IRD), infrared-assisted hot-air drying (IR-HAD), pulsed-vacuum drying (PVD), and vacuum freeze-drying (VFD) on the drying kinetics, microstructure, physicochemical properties (color, non-enzyme browning index, and rehydration ratio), and total phenol, total flavonoid, and ascorbic acid contents of sea buckthorn berries. The results showed that the IR-HAD time was the shortest, followed by the HAD, IRD, and PVD times, whereas the VFD time was the longest. The value of the color parameter L* decreased from 53.44 in fresh sea buckthorn berries to 44.18 (VFD), 42.60 (PVD), 37.58 (IRD), 36.39 (HAD), and 36.00 (IR-HAD) in dried berries. The browning index also showed the same trend as the color change. Vacuum freeze-dried berries had the lowest browning index (0.24 Abs/g d.m.) followed by that of pulsed-vacuum-(0.28 Abs/g d.m.), infrared- (0.35 Abs/g d.m.), hot-air-(0.42 Abs/g d.m.), and infrared-assisted hot-air-dried berries (0.59 Abs/g d.m.). The ascorbic acid content of sea buckthorn berries decreased by 45.39, 53.81, 74.23, 77.09, and 79.93% after VFD, PVD, IRD, IR-HAD, and HAD, respectively. The vacuum freeze-dried and pulsed-vacuum-dried sea buckthorn berries had better physicochemical properties than those dried by HAD, IRD, and IR-HAD. Overall, VFD and PVD had the highest ascorbic acid and total phenolic contents, good rehydration ability, and bright color. Nonetheless, considering the high cost of VFD, we suggest that PVD is an optimal drying technology for sea buckthorn berries, with the potential for industrial application.

Metabolomics analysis unveils important changes involved in the salt tolerance of Salicornia europaea

Salicornia europaea is one of the world's salt-tolerant plant species and is recognized as a model plant for studying the metabolism and molecular mechanisms of halophytes under salinity. To investigate the metabolic responses to salinity stress in S. europaea, this study performed a widely targeted metabolomic analysis after analyzing the physiological characteristics of plants exposed to various NaCl treatments. S. europaea exhibited excellent salt tolerance and could withstand extremely high NaCl concentrations, while lower NaCl conditions (50 and 100 mM) significantly promoted growth by increasing tissue succulence and maintaining a relatively stable K⁺ concentration. A total of 552 metabolites were detected, 500 of which were differently accumulated, mainly consisting of lipids, organic acids, saccharides, alcohols, amino acids, flavonoids, phenolic acids, and alkaloids. Sucrose, glucose, p-proline, quercetin and its derivatives, and kaempferol derivatives represented core metabolites that are responsive to salinity stress. Glycolysis, flavone and flavonol biosynthesis, and phenylpropanoid biosynthesis were considered as the most important pathways responsible for salt stress response by increasing the osmotic tolerance and antioxidant activities. The high accumulation of some saccharides, flavonoids, and phenolic acids under 50 mM NaCl compared with 300 mM NaCl might contribute to the improved salt tolerance under the 50 mM NaCl treatment. Furthermore, quercetin, quercetin derivatives, and kaempferol derivatives showed varied change patterns in the roots and shoots, while coumaric, caffeic, and ferulic acids increased significantly in the roots, implying that the coping strategies in the shoots and roots varied under salinity stress. These findings lay the foundation for further analysis of the mechanism underlying the response of S. europaea to salinity.

Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches

Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.

Antioxidant capacity, phytochemical profiles, and phenolic metabolomics of selected edible seeds and their sprouts

Sprouts are recognized as nutritional and functional vegetables. In this study, 17 selected seeds were germinated simultaneously. The antioxidant capacity and total phenolic content (TPC) were determined for seeds and sprouts of all species. Both seed and sprout of white radish, with the highest antioxidant capacity, and TPC among all the 17 species, were further determined for phenolic metabolomics. Four phenolic classes with 316 phenolic metabolites were identified. 198 significantly different metabolites with 146 up-regulated and 52 down-regulated were confirmed, and high amounts of phenolic acids and flavonoids were found to be accumulated in the sprout. Several metabolism and biosynthesis, including phenylpropanoid, favone and flavonol, phenylalanine, and various secondary metabolites, were significantly activated. Significant correlations were found among FRAP, DPPH, ABTS, TPC, and phenolic profiles. Therefore, white radish sprout could be served as antioxidant and could be a good source of dietary polyphenols.

Selenate and selenite transporters in proso millet: Genome extensive detection and expression studies under salt stress and selenium

Crops are susceptible to a variety of stresses and amongst them salinity of soil is a global agronomic challenge that has a detrimental influence on crop yields, thus posing a severe danger to our food security. Therefore, it becomes imperative to examine how plants respond to salt stress, develop a tolerance that allows them to live through higher salt concentrations and choose species that can endure salt stress. From the perspective of food, security millets can be substituted to avoid hardships because of their efficiency in dealing with salt stress. Besides, this problem can also be tackled by using beneficial exogenous elements. Selenium (Se) which exists as selenate or selenite is one such cardinal element that has been reported to alleviate salt stress. The present study aimed for identification of selenate and selenite transporters in proso millet (Panicum miliaceum L.), their expression under NaCl (salt stress) and Na₂SeO₃ (sodium selenite)treatments. This study identified eight transporters (RLM65282.1, RLN42222.1, RLN18407.1, RLM74477.1, RLN41904.1, RLN17428.1, RLN17268.1, RLM65753.1) that have a potential role in Se uptake in proso millet. We analyzed physicochemical properties, conserved structures, sub-cellular locations, chromosome location, molecular phylogenetic analysis, promoter regions prediction, protein-protein interactions, three-dimensional structure modeling and evaluation of these transporters. The analysis revealed the chromosome location and the number of amino acids present in these transporters as RLM65282.1 (16/646); RLN42222.1 (1/543); RLN18407.1 (2/483); RLM74477.1 (15/474); RLN41904.1 (1/521); RLN17428.1 (2/522); RLN17268.1(2/537);RLM65753.1 (16/539). The sub-cellular locations revealed that all the selenite transporters are located in plasma membrane whereas among selenate transporters RLM65282.1 and RLM74477.1 are located in mitochondria and RLN42222.1 and RLN18407.1 in chloroplast. The transcriptomic studies revealed that NaCl stress decreased the expression of both selenate and selenite transporters in proso millet and the applications of exogenous 1µM Se (Na₂SeO₃) increased the expression of these Se transporter genes. It was also revealed that selenate shows similar behavior as sulfate, while selenite transport resembles phosphate. Thus, it can be concluded that phosphate and sulphate transporters in millets are responsible for Se uptake.

Polyphenol Composition and Antioxidant Activity of Japonica Rice Cultivars and Intake Status

Japonica rice is produced mainly in northeast China, Japan, and the Korean Peninsula. Polyphenols and flavonoids are the main antioxidants in japonica rice. This study reported the polyphenol content and antioxidant activity of nine brown and white japonica rice cultivars. The total phenolic and flavonoid contents of brown rice were in the ranges of 241.98-296.76 GAE mg/100 g, and 225.30-276.80 RE mg/100 g, respectively. These values were significantly higher than that of white rice by 118.98-206.06% and 135.0-217%, respectively. The bound fraction from phenolics and flavonoids contributed 41.1-63.6% and 62.22-78.19% of the total phenolic and flavonoid content in brown rice, respectively, while these ranges were 55.5-73.5% and 46.07-66.83% in white rice, respectively. p-Hydroxybenzonic acid was the predominant phenolic acid in japonica rice. All four antioxidant capacities of brown rice (DPPH, ABTS, OH, FRAP) were higher by up to 1.68-2.85 times than those of white rice. The PZ21 (Yanfeng 47) japonica rice variety has outstanding antioxidant capacity based on the weights of each antioxidant index. According to the differences of functional substances among varieties, it can provide guidance for consumers and theoretical basis for the production of healthy food.

Insights into the Jasmonate Signaling in Basal Land Plant Revealed by the Multi-Omics Analysis of an Antarctic Moss Pohlia nutans Treated with OPDA

12-oxo-phytodienoic acid (OPDA) is a biosynthetic precursor of jasmonic acid and triggers multiple biological processes from plant development to stress responses. However, the OPDA signaling and relevant regulatory networks were largely unknown in basal land plants. Using an integrated multi-omics technique, we investigated the global features in metabolites and transcriptional profiles of an Antarctic moss (Pohlia nutans) in response to OPDA treatment. We detected 676 metabolites based on the widely targeted metabolomics approach. A total of 82 significantly changed metabolites were observed, including fatty acids, flavonoids, phenolic acids, amino acids and derivatives, and alkaloids. In addition, the transcriptome sequencing was conducted to uncover the global transcriptional profiles. The representative differentially expressed genes were summarized into functions including Ca2+ signaling, abscisic acid signaling, jasmonate signaling, lipid and fatty acid biosynthesis, transcription factors, antioxidant enzymes, and detoxification proteins. The integrated multi-omics analysis revealed that the pathways of jasmonate and ABA signaling, lipid and fatty acid biosynthesis, and flavonoid biosynthesis might dominate the molecular responses to OPDA. Taken together, these observations provide insights into the molecular evolution of jasmonate signaling and the adaptation mechanisms of Antarctic moss to terrestrial habitats.

Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis

Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.

Metabolic profiling and gene expression analyses provide insights into cold adaptation of an Antarctic moss Pohlia nutans

Antarctica is the coldest, driest, and most windy continent on earth. The major terrestrial vegetation consists of cryptogams (mosses and lichens) and two vascular plant species. However, the molecular mechanism of cold tolerance and relevant regulatory networks were largely unknown in these Antarctic plants. Here, we investigated the global alterations in metabolites and regulatory pathways of an Antarctic moss (Pohlia nutans) under cold stress using an integrated multi-omics approach. We found that proline content and several antioxidant enzyme activities were significantly increased in P. nutans under cold stress, but the contents of chlorophyll and total flavonoids were markedly decreased. A total of 559 metabolites were detected using ultra high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS). We observed 39 and 71 differentially changed metabolites (DCMs) after 24 h and 60 h cold stress, indicating that several major pathways were differentially activated for producing fatty acids, alkaloids, flavonoids, terpenoids, and phenolic acids. In addition, the quantitative transcriptome sequencing was conducted to uncover the global transcriptional profiles of P. nutans under cold stress. The representative differentially expressed genes (DEGs) were identified and summarized to the function including Ca²⁺ signaling, ABA signaling, jasmonate signaling, fatty acids biosynthesis, flavonoid biosynthesis, and other biological processes. The integrated dataset analyses of metabolome and transcriptome revealed that jasmonate signaling, auxin signaling, very-long-chain fatty acids and flavonoid biosynthesis pathways might contribute to P. nutans acclimating to cold stress. Overall, these observations provide insight into Antarctic moss adaptations to polar habitats and the impact of global climate change on Antarctic plants.

Metabarcoding and Metabolome Analyses Reveal Mechanisms of Leymus chinensis Growth Promotion by Fairy Ring of Leucocalocybe mongolica

Fairy rings are a unique ecological phenomenon caused by the growth of the fungal mycelium in the soil. Fairy rings formed by Leucocalocybe mongolica (LM) are generally distributed in the Mongolian Plateau, where they promote plant growth without fertilization and alleviate fertilizer use. We previously investigated the soil factors regulating growth promotion in a fairy ring ecosystem; however, the aspects of the plant (Leymus chinensis, LC) that promote growth have not been explored. Therefore, the present study investigated the endophyte diversity and metabolome of LC in an LM fairy ring ecosystem. We analyzed the leaf and root samples of LC from the DARK (FR) and OUT (CK) zones. The fairy rings significantly improved the fungal diversity of roots and leaves and the bacterial diversity of leaves in the FR zone. Ralstonia was the dominant bacteria detected in the LC leaves. In addition, Marasmius, another fairy ring fungal genus, was also detected with a high abundance in the roots of the FR zone. Furthermore, widely targeted metabolome analysis combined with KEGG annotation identified 1011 novel metabolites from the leaves and roots of LC and seven pathways significantly regulated by the fairy ring in the FR zone. The fairy ring ecosystem significantly downregulated the flavonoid metabolism in the leaves and roots of LC. The correlation analysis found Ralstonia is a potential regulatory factor of flavonoid biosynthesis in LC. In addition, salicylic acid and jasmonic acid were found upregulated in the leaves, probably related to Marasmius enrichment. Thus, the study details plant factors associated with enhanced growth in an LM fairy ring ecosystem. These findings lay a theoretical foundation for developing the fairy ring ecosystem in an agricultural system.

Widely targeted metabolomics reveals stamen petaloid tissue of Paeonia lactiflora Pall. being a potential pharmacological resource

Paeonia lactiflflora Pall. has a long edible and medicinal history because of the very high content of biologically active compounds. However, little information is available about the metabolic basis of pharmacological values of P. lactiflora flowers. In this study, we investigated metabolites in the different parts of P. lactiflora flowers, including petal, stamen petaloid tissue and stamen, by widely targeted metabolomics approach. A total of 1102 metabolites were identified, among which 313 and 410 metabolites showed differential accumulation in comparison groups of petal vs. stamen petaloid tissue and stamen vs. stamen petaloid tissue. Differential accumulated metabolites analysis and KEGG pathway analysis showed that the flavonoids were the most critical differential metabolites. Furthermore, difference accumulation of flavonoids, phenolic acids, tannins and alkaloids might lead to the differences in antioxidant activities and tyrosinase inhibition effects. Indeed, stamen petaloid tissue displayed better antioxidant and anti-melanin production activities than petal and stamen through experimental verification. These results not only expand our understanding of metabolites in P. lactiflora flowers, but also reveal that the stamen petaloid tissues of P. lactiflora hold the great potential as promising ingredients for pharmaceuticals, functional foods and skincare products.

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana

Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.

Variation in Phenolic, Mineral, Dietary Fiber, and Antioxidant Activity across Southern Tunisian Pearl Millet Germplasm

Pearl millet crop, reputed as one of the most important food sources cultivated in arid and semiarid parts of Africa and Asia, is known to be a source of many bioactive molecules with potential health-promoting properties. In Tunisia, this crop presented historically rich and diversified germplasm, which is being threatened by genetic erosion. The preservation programs of these species have been held for more than 20 years via participatory breeding schemes. A prospection was undertaken to collect pearl millet cultivars preserved in the last two decades from south-eastern Tunisian farmers to estimate their variability and performances. The aim of this study was to assess the profiles of phenolic compounds, antioxidant capacities, mineral composition, and dietary fiber contents of ten pearl millet cultivars in south-eastern Tunisia. The total phenolics and flavonoids in the free fraction ranged from 506.33 to 1287.71 µg.g−1 DM ferulic acid equivalent (FAE) and 4.17 to 12.53 µg.g−1 DM catechin equivalent (CE), respectively. The highest polyphenolic content from all genotypes was 1134.96 µg·g−1 DM (genotype Med.AG1.3). LC-MS analysis of individual phenol compounds allowed the identification of eight phenolic acids in millet grains. The quinic acid, p-coumaric acid, and caffeic acid were predominant phenolic acids, and six flavonoid compounds with cirsiliol and silymarin were the predominant flavonoids. The ranges of mineral contents variation were 693.10 to 1075.40 and 80.75 to 175.40 μg·g−1 for Ca and Mg, respectively, and 9.55 to 32.80, 0.75 to 8.60, 1.84 to 12.21, and 3.63 to 11.40 μg·g−1 for Na, Zn, Cu, and Fe, respectively. The content of NDF, ADF, and ADL per dry weight varied from 20 to 31%, 1 to 4.2%, and 0.4 to 2.3%, respectively. Overall, considering the variability among the assessed attributes, heatmap analysis showed the association between each of the traits as related to the clustered genotypes.

Differential Flavonoids and Carotenoids Profiles in Grains of Six Poaceae Crops

Poaceae practically dominate staple crops for humans. In addition to the issue of sustenance, there is a growing interest in the secondary metabolites of these staple crops and their functions on health. In this study, metabolomic variations were investigated among six important species of Poaceae with a total of 17 cultivars, including wheat, maize, rice, sorghum, foxtail millet, and broomcorn millet. A total of 201 flavonoid metabolites and 29 carotenoid metabolites were identified based on the UPLC-ESI-MS/MS system. Among them, 114, 128, 101, 179, 113, and 92 flavonoids and 12, 22, 17, 15, 21, and 18 carotenoids were found in wheat, maize, rice, sorghum, foxtail millet, and broomcorn millet, respectively. Only 46 flavonoids and 8 carotenoids were shared by the six crops. Crop-specific flavonoids and carotenoids were identified. Flavone, anthocyanins, flavanone and polyphenol were the major metabolite differences, which showed species specificity. The flavonoid content of the grains from 17J1344 (sorghum), QZH and NMB (foxtail millet) and carotenoids from Mo17 (maize) were higher than the other samples. This study provides a better knowledge of the differences in flavonoid and carotenoid metabolites among Poaceae crops, as well as provides a theoretical basis for the identification of functional metabolites in these grains.

Comparative metabolomics analysis of pericarp from four varieties of Zanthoxylum bungeanum Maxim

A qualitative and quantitative analysis of metabolites was performed by metabolomics comparation on the pericarps of four varieties of Zanthoxylum bungeanum Maxim. The Zanthoxylum bunganum as scion combined with three rootstock varieties of Zanthoxylum piasezkii Maxim (YJ), July Zanthoxylum bunganum Maxim (QJ), and August Zanthoxylum bunganum Maxim (BJ), at the same time Zanthoxylum bungeanum seedlings breeding were compared as control (MJ). A total of 1429 metabolites were identified in Zanthoxylum bungeanum Maxim pericarps based on chromatography and mass spectrometry dual detection platform. While the metabolites between four varieties of Z. bungeanum varied, there was identified 31, 15, 7, 79, 42, 19 down-regulated and 55, 50, 13, 75, 43, 27 up-regulated differential metabolites between MJ and BJ, MJ and QJ, MJ and YJ, QJ and BJ, YJ and BJ, YJ and QJ. Meanwhile, the differential metabolites composition was distinct among various varieties of Z. bungeanum and dominant by phenolic compounds flavonoid and phenolic acids, especially highest in varieties July Zanthoxylum bunganum Maxim. Highlight A comparative metabolomics analyzed in four varieties of Zanthoxylum bungeanum pericarp.Total 1429 metabolites were identified and mainly in flavonoid and phenolic acid.July and August Zanthoxylum bunganum Maxim has highest antioxidant capacity.The rootstock July Zanthoxylum bunganum Maxim was recommended in Loess Plateau.

Improvement of antioxidant properties of jujube puree by biotransformation of polyphenols via Streptococcus thermophilus fermentation

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Streptococcus thermophilus enriched polyphenols in fermented jujube puree.

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Fermentation improved jujube puree DPPH scavenging capability by 26%.

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12 phenolics were identified as differential metabolites.

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Fermentation could be a promising approach to improve jujube phenolic quality.

To investigate the effect of lactic acid bacteria fermentation on jujube bioactivity, Streptococcus thermophilus was used to ferment jujube puree. The number of viable bacteria cells, physicochemical properties, phenolics profile and antioxidant capacity were analyzed, and their correlation were investigated. Streptococcus thermophilus exhibited a high growth capacity in jujube puree, and significantly (p < 0.05) increased the total phenolics content, 2,2-Diphenyl-1-picrylhydrazyl (DPPH) scavenging activity and reducing power after 48 h fermentation, while 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) scavenging activity was decreased. 12 differentially metabolized polyphenols were identified in fermented jujube puree. Upregulated phenolics exhibited a positive correlation with DPPH radical-scavenging ability and reducing power. This work demonstrated that Streptococcus thermophilus fermentation can be an effective method with great practical application potential to improve the antioxidant activity in jujube puree by modifying the phenolic compositional quantity and quality.

Identifying Key Metabolites Associated with Glucosinolate Biosynthesis in Response to Nitrogen Management Strategies in Two Rapeseed (Brassica napus) Varieties

A high glucosinolate (GSL) concentration, an undesirable substance, has severely restricted rapeseed (Brassica species) development. We performed widely targeted metabolomics analysis based on the ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) technology to analyze the metabolic profiles and identify the differential metabolites and GSL components in response to different nitrogen (N) levels in two rapeseed varieties. A total of 341 metabolites and 38 GSL components were detected in the seeds. A total of 188 differential metabolites, including 34 GSL components, were identified in response to different treatments, which were mapped into 2-oxocarboxylic acid metabolism, tryptophan metabolism, and GSL biosynthesis. Key indicators of GSL components highly responsible for different N levels under two contrasting varieties were recognized, i.e., 1-methylpropyl GSL and 4-methylthiobutyl GSL. This study suggests that the efficient N management and variety selection are important strategies for developing rapeseed with low GSLs.

Metabolomics Analysis Revealed the Characteristic Metabolites of Hemp Seeds Varieties and Metabolites Responsible for Antioxidant Properties

Hemp seeds are rich in metabolites such as protein, lipids and flavonoids, which are beneficial to health and can be used as a nutritional supplement. Few studies have focused on the metabolites of different hemp seed varieties. In the current study, using widely targeted metabolomics based on UHPLC-QQQ-MS/MS, we compared the metabolomes of seeds from seven hemp varieties with different uses. A total of 1,001 metabolites, including 201 flavonoids, 86 alkaloids, and 149 phenolic acids, were identified. Flavonoids, organic acids, alkaloids, lipids, and fatty acids with high nutritional value are important to investigate the differences between hemp accessions. By using weighted gene co-expression network analysis (WGCNA), six modules of closely related metabolites were identified. And, we identified the metabolite characteristics and hub metabolites of each variety. Then, we experimentally determined antioxidant activity of seven varieties and demonstrated that alkaloids, flavonoids, phenolic acids, terpenes, and free fatty acids are responsible for the antioxidant activity of hemp seeds. Our research provides useful information for further investigation of the chemical composition of hemp seeds.

The Antarctic Moss Pohlia nutans Genome Provides Insights Into the Evolution of Bryophytes and the Adaptation to Extreme Terrestrial Habitats

The Antarctic continent has extreme natural environment and fragile ecosystem. Mosses are one of the dominant floras in the Antarctic continent. However, their genomic features and adaptation processes to extreme environments remain poorly understood. Here, we assembled the high-quality genome sequence of the Antarctic moss (Pohlia nutans) with 698.20 Mb and 22 chromosomes. We found that the high proportion of repeat sequences and a recent whole-genome duplication (WGD) contribute to the large size genome of P. nutans when compared to other bryophytes. The genome of P. nutans harbors the signatures of massive segmental gene duplications and large expansions of gene families, likely facilitating neofunctionalization. Genomic characteristics that may support the Antarctic lifestyle of this moss comprise expanded gene families involved in phenylpropanoid biosynthesis, unsaturated fatty acid biosynthesis, and plant hormone signal transduction. Additional contributions include the significant expansion and upregulation of several genes encoding DNA photolyase, antioxidant enzymes, flavonoid biosynthesis enzymes, possibly reflecting diverse adaptive strategies. Notably, integrated multi-omic analyses elucidate flavonoid biosynthesis may function as the reactive oxygen species detoxification under UV-B radiation. Our studies provide insight into the unique features of the Antarctic moss genome and their molecular responses to extreme terrestrial environments.

Multiomics Analyses of Two Sorghum Cultivars Reveal the Molecular Mechanism of Salt Tolerance

Sorghum [Sorghum bicolor (L.) Moench] is one of the most important cereal crops and contains many health-promoting substances. Sorghum has high tolerance to abiotic stress and contains a variety of flavonoids compounds. Flavonoids are produced by the phenylpropanoid pathway and performed a wide range of functions in plants resistance to biotic and abiotic stress. A multiomics analysis of two sorghum cultivars (HN and GZ) under different salt treatments time (0, 24, 48, and 72) was performed. A total of 45 genes, 58 secondary metabolites, and 246 proteins were recognized with significant differential abundances in different comparison models. The common differentially expressed genes (DEGs) were allocated to the "flavonoid biosynthesis" and "phenylpropanoid biosynthesis" pathways. The most enriched pathways of the common differentially accumulating metabolites (DAMs) were "flavonoid biosynthesis," followed by "phenylpropanoid biosynthesis" and "arginine and proline metabolism." The common differentially expressed proteins (DEPs) were mainly distributed in "phenylpropanoid biosynthesis," "biosynthesis of cofactors," and "RNA transport." Furthermore, considerable differences were observed in the accumulation of low molecular weight nonenzymatic antioxidants and the activity of antioxidant enzymes. Collectively, the results of our study support the idea that flavonoid biological pathways may play an important physiological role in the ability of sorghum to withstand salt stress.

Comparison of nutritional compositions of foxtail millet from the different cultivation regions by UPLC-Q-Orbitrap HRMS based metabolomics approach

Foxtail millet (Setaria italica (L.) P. Beauv) is cultivated throughout most parts of Shanxi province. Although quite a number of reports have been conducted on the bioactivities of foxtail millet, little information was available on the metabolite differences of the foxtail millet seeds from different cultivation regions. In this study, a systematic study on the metabolite composition of the foxtail millet seed from Shanxi province was conducted by ultra-high performance liquid chromatography combined with electrospray ionization quadrupole/orbitrap high-resolution mass spectrometry, and 158 compounds were characterized through analysis of mass fragmentation patterns and comparison with the data in the databases and literatures. Then the metabolomic analysis, in combination with heatmap and hierarchical clustering analysis revealed the significant differences between the foxtail millet from northern and southern Shanxi province, which was ascribed to 20 differential metabolites. Then metabolic pathway analysis was performed based on these differential metabolites, and three metabolic pathways were selected as the key contributors. The results showed that foxtail millet from different cultivation regions showed obvious metabolite differences, which was probably related to environmental factors. In addition, the findings also provide an important reference for further research on the functional food development from foxtail millet. PRACTICAL APPLICATIONS: Foxtail millet (Setaria italica (L.) P. Beauv) as a staple food among the majority of people, is rich in bioactive nutrients, including free fatty acids, triglycerides, cellulose, protein, vitamins, and polyphenol, et al. The metabolite composition of the foxtail millet seed was investigated systematically and the results showed that the climate conditions can directly affect the metabolite composition of foxtail millets, and provided important reference for the further research on the resource utilization and functional food development from foxtail millet.