Comparative metabolic profiling of cultivated and wild black soybeans reveals distinct metabolic alterations associated with their domestication

Metabolic profiling and spatial metabolite distribution in wild soybean (G. soja) and cultivated soybean (G. max) seeds

Wild soybeans retain many substances significantly reduced or lost in cultivars during domestication. This study utilized LC-MS to analyze metabolites in the seed coats and embryos of wild and cultivated soybeans. 866 and 815 metabolites were identified in the seed extracts of both soybean types, with 35 and 10 significantly differing metabolites in the seed coat and embryos, respectively. The upregulated metabolites in wild soybeans are linked to plant defense, stress responses, and nitrogen cycling. MALDI-MSI results further elucidated the distribution of these differential metabolites in the cotyledons, hypocotyls, and radicles. In addition to their role in physiological processes like growth and response to environmental stimuli, the prevalent terpenoids, lipids, and flavonoids present in wild soybeans exhibit beneficial bioactivities, including anti-inflammatory, antibacterial, anticancer, and cardiovascular disease prevention properties. These findings underscore the potential of wild soybeans as a valuable resource for enhancing the nutritional and ecological adaptability of cultivated soybeans.

Flavonoid localization in soybean seeds: Comparative analysis of wild (Glycine soja) and cultivated (Glycine max) varieties

Wild soybean (Glycine soja) is known for its high flavonoid contents, yet the distribution of flavonoids in the seeds is not well understood. Herein, we utilized matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and metabolomics methods to systematically investigate flavonoid differences in the seed coats and embryos of G. soja and G. max. The results of flavonoid profiles and total flavonoid content analyses revealed that flavonoid diversity and abundance in G. soja seed coats were significantly higher than those in G. max whereas the levels were similar in embryos. Specifically, 23 unique flavonoids were identified in the seed coats of G. soja, including procyanidins, epicatechin derivatives, and isoflavones. Using MALDI-MSI, we further delineated the distribution of the important flavonoids in the cotyledons, hypocotyls, and radicles of the two species. These findings imply that G. soja holds considerable breeding potential to enhance the nutritional and stress resistance traits of G. max.

An Untargeted Metabolomics Approach to Study the Variation between Wild and Cultivated Soybeans

The differential metabolite profiles of four wild and ten cultivated soybeans genotypes were explored using an untargeted metabolomics approach. Ground soybean seed samples were extracted with methanol and water, and metabolic features were obtained using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) in both positive and negative ion modes. The UHPLC-HRMS analysis of the two different extracts resulted in the putative identification of 98 metabolites belonging to several classes of phytochemicals, including isoflavones, organic acids, lipids, sugars, amino acids, saponins, and other compounds. The metabolic profile was significantly impacted by the polarity of the extraction solvent. Multivariate analysis showed a clear difference between wild and cultivated soybean cultivars. Unsupervised and supervised learning algorithms were applied to mine the generated data and to pinpoint metabolites differentiating wild and cultivated soybeans. The key identified metabolites differentiating wild and cultivated soybeans were isoflavonoids, free amino acids, and fatty acids. Catechin analogs, cynaroside, hydroxylated unsaturated fatty acid derivatives, amino acid, and uridine diphosphate-N-acetylglucosamine were upregulated in the methanol extract of wild soybeans. In contrast, isoflavonoids and other minor compounds were downregulated in the same soybean extract. This metabolic information will benefit breeders and biotechnology professionals to develop value-added soybeans with improved quality traits.

An integrated untargeted metabolomic approach reveals the quality characteristics of black soybeans from different geographical origins in China

Black soybeans are extensively planted and consumed in China due to their high nutritional value and numerous health benefits. However, very few is known about the characteristic metabolites of black soybeans from different geographical origins in China. In the present study, 31 black soybean samples were collected from 11 main producing provinces in China. A combined metabolomics approach using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and gas chromatography coupled to an Orbitrap mass analyzer (GC-orbitrap-MS) was performed for the first time to comprehensively investigate the metabolite variability among the black soybeans from different geographical origins. A total of 48 differential non-volatile metabolites and 14 differential volatile metabolites were identified based on orthogonal partial least squares discriminant analysis (OPLS-DA) coupled with analysis of variance (ANOVA). Higher procyanidin B1, procyanidin B2, epicatechin, malonylated isoflavones, and β-pinene were observed in Gansu black soybeans. Guangxi black soybeans had higher amounts of linoleic acid and its oxidation products of hexanal and pentane. The black soybeans from Xinjiang and Yunnan were found to have higher delphinidin-derived anthocyanins, gamma-glutamyl peptides, and aromatic hydrocarbons. The characteristic metabolites of black soybeans from other geographical origins were also clarified. This study indicated that the integrated untargeted metabolomic approach can be a powerful tool to provide knowledge for developing specialty black soybeans.

Metabolomic Analysis Reveals Domestication-Driven Reshaping of Polyphenolic Antioxidants in Soybean Seeds

Crop domestication has resulted in nutrient losses, so evaluating the reshaping of phytonutrients is crucial for improving nutrition. Soybean is an ideal model due to its abundant phytonutrients and wild relatives. In order to unravel the domestication consequence of phytonutrients, comparative and association analyses of metabolomes and antioxidant activities were performed on seeds of six wild (Glycine soja (Sieb. and Zucc.)) and six cultivated soybeans (Glycine max (L.) Merr.). Through ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), we observed a greater metabolic diversity in wild soybeans, which also displayed higher antioxidant activities. (-)-Epicatechin, a potent antioxidant, displayed a 1750-fold greater abundance in wild soybeans than in cultivated soybeans. Multiple polyphenols in the catechin biosynthesis pathway were significantly higher in wild soybeans, including phlorizin, taxifolin, quercetin 3-O-galactoside, cyanidin 3-O-glucoside, (+)-catechin, (-)-epiafzelechin, catechin-glucoside, and three proanthocyanidins. They showed significant positive correlations with each other and antioxidant activities, indicating their cooperative contribution to the high antioxidant activities of wild soybeans. Additionally, natural acylation related to functional properties was characterized in a diverse range of polyphenols. Our study reveals the comprehensive reprogramming of polyphenolic antioxidants during domestication, providing valuable insights for metabolism-assisted fortification of crop nutrition.

Proliferation and Metabolic Profiling of Cynanchum wilfordii Adventitious Roots Using Explants from Different Cultivation Methods

Cynanchum wilfordii root is used in traditional herbal medicine owing to its various pharmacological activities. However, C. wilfordii roots are misused owing to their morphological similarities with C. auriculatum. Adventitious root (AR) culture can prevent such misuse, and the selection of plant materials is an important procedure for producing high-quality ARs. This study aimed to compare the proliferation and metabolic profiles of C. wilfordii ARs in two types of explants from different cultivation methods (either cultivated in open field (ECF) or cultivated on a heap of C. wilfordii (ECH)). After 4 weeks of culture, the proliferation rate and number and length of secondary ARs were determined, and 3/4 Murashige and Skoog (MS) salt medium, 4.92 μM indole-3-butyric acid (IBA), and 5% sucrose were suggested as the best proliferation conditions for ARs originating from both ECF and ECH. Through metabolic profiling, ARs from ECH were found to show higher accumulation patterns for flavonoids, polysaccharides, hydroxyacetophenones, aromatic amino acids, and mono-unsaturated fatty acids, which were ascribed to the activation of flavonoid biosynthesis, the phenylpropanoid pathway, and fatty acid desaturase, stimulated by abiotic stresses. In contrast, ARs from ECF had higher levels of TCA cycle intermediates, amino acids in the aspartate-glutamate pathway, and saturated and polyunsaturated fatty acids, indicating energy metabolism and plant development. Overall, the current study provided information on the optimal conditions for inducing C. wilfordii ARs with higher amounts of bioactive compounds.

Exploring chemical diversity in Glycine max cultivars: A multivariate approach in the search for bioactive compounds against Spodoptera cosmioides

Soybean crop is regulated by abiotic and biotic stresses with great potential in reducing grain yield and quality. The selection of resistant cultivars is a promising approach for mitigating these damages. We evaluated the chemical profile of Glycine max leaves from different cultivars in order to explore their defense mechanisms against Spodoptera cosmioides caterpillars. We optimized solid-liquid extraction techniques using ultrasound bath and static headspace extraction. Additionally, we developed an approach based on liquid and gas chromatography for analyzing the chemical profile of G. max cultivars. The principal component analysis allowed the classification of transgenic cultivars, which are classified as susceptible to S. cosmioides, from those obtained by genetic improvement and resistant to the insect. Differences were observed in the abundance of phenolic glycosides, lipids, aldehydes, and alcohols. More specifically, S. cosmioides resistant cultivars presented molecules related to the jasmonic and salicylic acid pathways. Such data can contribute to a molecular understanding of phenotypic diversity in soybean cultivars, from plant quality to resistance mechanisms and adaptation, to environmental stress and herbivory.

Multiomics understanding of improved quality in cherry radish (Raphanus sativus L. var. radculus pers) after foliar application of selenium nanomaterials

A selenium (Se)-nanoenabled agriculture strategy was established in this work to improve crop yield and quality. The results demonstrated that Se engineering nanomaterials (Se ENMs, 10 mg·L^-1) were absorbed and translocated in cherry radish (Raphanus sativus L. var. radculus pers) from shoots to taproots after foliar application. RNA-Seq and metabolomic results indicated that the glucolysis, pyruvate and tricarboxylic acid (TCA) cycle metabolism pathways were accelerated by exposure to Se ENMs, resulting in increased production of flavonoids (3.2-fold), amino acids (1.4-fold), and TCA (2.5-fold) compared with the control. Moreover, Se content was enhanced by 5.4 and 2.6 times in pericarp and pulp upon Se ENMs exposure, respectively, which was more efficient (2.2 and 1.1 times) than SeO₃^2- treatment. Additionally, the yield of cherry radish was increased by 67.6% under Se ENMs, whereas SeO₃^2- exposure only led to an increase of 7.4%. Therefore, the application of Se ENMs could reduce the amount of fertilizer used to minimize the environmental impact in agriculture while improve crop production and quality. These findings highlighted the significant potential of Se ENMs-enabled agriculture practices as an eco-friendly and sustainable crop strategy.

Extract from Black Soybean Cultivar A63 Extract Ameliorates Atopic Dermatitis-like Skin Inflammation in an Oxazolone-Induced Murine Model

Black soybean has been used in traditional medicine to treat inflammatory diseases, cancer, and diabetes and as a nutritional source since ancient times. We found that Korean black soybean cultivar A63 has more cyanidin-3-O-glucoside, (C3G), procyanidin B2 (PB2), and epicatechin (EPC) contents than other cultivars and has beneficial effects on cell viability and anti-oxidation. Given the higher concentration of anthocyanidins and their strong anti-oxidant activity, we predicted that A63 extract could relieve inflammatory disease symptoms, including those of atopic dermatitis (AD). Here, we evaluated the anti-AD activity of A63 extract in an oxazolone (OXA)-induced mouse model. A63 extract treatment significantly reduced epidermal thickness and inflammatory cell infiltration, downregulated the expression of AD gene markers, including Interleukin (IL)-4 and IL-5, and restored damaged skin barrier tissues. Furthermore, A63 extract influenced the activation of the signal transducer and activator of transcription (STAT) 3 and STAT6, extracellular regulatory kinase (ERK), and c-Jun N-terminal kinase (JNK) signaling pathways, which play a crucial role in the development of AD. Altogether, our results suggest that A63 can ameliorate AD-like skin inflammation by inhibiting inflammatory cytokine production and STAT3/6 and Mitogen-activated protein kinase (MAPK) signaling and restoring skin barrier function.

Profiles of Essential Oils and Correlations with Phenolic Acids and Primary Metabolites in Flower Buds of Magnolia heptapeta and Magnolia denudata var. purpurascens

Magnolia flower buds are a source of herbal medicines with various active compounds. In this study, differences in the distribution and abundance of major essential oils, phenolic acids, and primary metabolites between white flower buds of Magnolia heptapeta and violet flower buds of Magnolia denudata var. purpurascens were characterised. A multivariate analysis revealed clear separation between the white and violet flower buds with respect to primary and secondary metabolites closely related to metabolic systems. White flower buds contained large amounts of monoterpene hydrocarbons (MH), phenolic acids, aromatic amino acids, and monosaccharides, related to the production of isoprenes, as MH precursors, and the activity of MH synthase. However, concentrations of β-myrcene, a major MH compound, were higher in violet flower buds than in white flower buds, possibly due to higher threonine levels and low acidic conditions induced by comparatively low levels of some organic acids. Moreover, levels of stress-related metabolites, such as oxygenated monoterpenes, proline, and glutamic acid, were higher in violet flower buds than in white flower buds. Our results support the feasibility of metabolic profiling for the identification of phytochemical differences and improve our understanding of the correlated biological pathways for primary and secondary metabolites.

Metabolomic Variability of Different Soybean Genotypes: β-Carotene-Enhanced (Glycine max), Wild (Glycine soja), and Hybrid (Glycine max × Glycine soja) Soybeans

We obtained a new hybrid soybean (Hybrid) by hybridizing β-carotene-enhanced soybean (BCE; Glycine max L.) containing the phytoene synthase-2A-carotene desaturase gene and wild-type soybean (Wild; Glycine soja). To investigate metabolic changes between variants, we performed metabolic profiling of leaves (three growth stages) and seeds. Multivariate analyses revealed significant metabolic differences between genotypes in seeds and leaves, with seeds showing accumulation of phytosterols, tocopherols, and carotenoids (BCE only), indicating co-induction of the methylerythritol 4-phosphate and mevalonic acid pathways. Additionally, Hybrid produced intermediate levels of carotenoids and high levels of amino acids. Principal component analysis revealed metabolic discrimination between growth stages of soybean leaves and identified differences in leaf groups according to different genotypes at 8, 12, and 16 weeks, with Wild showing higher levels of environmental stress-related compounds relative to BCE and Hybrid leaves. The metabolic profiling approach could be a useful tool to identify metabolic links in various soybean cultivars.

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.

Metabolite Profiling Reveals Distinct Modulation of Complex Metabolic Networks in Non-Pigmented, Black, and Red Rice (Oryza sativa L.) Cultivars

Comprehensive profiling of primary and secondary metabolites was performed to understand metabolic differences associated with color formation in pigmented rice (Oryza sativa L.). Overall, 110 metabolites from non-pigmented, black, and red rice cultivars were identified. Black and red rice contained high levels of flavonoids associated with plant color. Black rice also contained high levels of terpenoids (carotenoids, tocopherols, phytosterols, and monoterpenes). The non-pigmented rice contained relatively low levels of secondary metabolites. Multivariate and pathway analyses were performed to data-mine the metabolite profiles. Hierarchical clustering analysis of correlation coefficients revealed metabolite clusters based on nitrogen and carbon sources. These clusters suggested a negative correlation between nitrogen and carbon. Pathway analysis revealed that black rice was rich in carbon-based secondary metabolites, with relatively low levels of primary metabolites compared with other rice cultivars. These data highlight the complex interactions between nitrogen and carbon metabolism of primary and secondary metabolites in rice. For the first time, the relationships and metabolic differences in terpenoid content (monoterpenes, triterpenes, and tetraterpenes) of non-pigmented and pigmented rice cultivars were analyzed. These findings should greatly contribute to the understanding of pigmented rice metabolome and inform breeding programs for new rice cultivars.

Comparison of Phenolic and Flavonoid Compound Profiles and Antioxidant and α-Glucosidase Inhibition Properties of Cultivated Soybean (Glycine max) and Wild Soybean (Glycine soja)

Wild soybean (Glycine soja Sieb.et Zucc; WS) has been used as a traditional food in China for many years and contains significantly higher levels of isoflavones than cultivated soybean (Glycine max; CS), but the secondary metabolites, including flavonoids and the phenolic composition differences between them, remain unclear. The results showed that WS possessed significantly higher total phenolic and flavonoid content and exhibited better antioxidant and α-glucosidase inhibition activities as well as excellent protective effects against H₂O₂-induced oxidative injury in a human endothelial cell line. Through metabolomic analysis, 642 metabolites were identified, and 238 showed differential expression, with 151 upregulated and 87 downregulated. A total of 79 flavonoid compounds were identified, 42 of which were upregulated in WS. 2'-Hydroxygenistein, garbanzol, protocatechuic aldehyde, ligustilide, and resveratrol were the most discriminated compounds in WS. The metabolic pathway analysis of differential metabolites related to the biosynthesis of flavonoids and phenolic acids were the biosynthesis of phenylpropanoids, flavonoids, isoflavonoids, flavones, and flavonols. This study substantially elucidated differences in the content of flavonoids and biological activities between WS and CS, which is useful information for the effective utilization of these two black soybean species in food processing.