Search Results (76)

Soybean (Glycine max [L.] Merr.) seed hardness is a critical physical trait that dictates processing efficiency and end-product quality, yet the underlying genetic and metabolic regulatory networks remain poorly elucidated. To systematically decipher the mechanisms governing this complex quantitative trait, a multi-omics approach integrating a genome-wide association study (GWAS), transcriptomics, and metabolomics was conducted on a panel of 162 soybean germplasm accessions from Northeast China. Four significant quantitative trait nucleotides (QTNs) on chromosomes 15 and 19 were identified by GWAS. Subsequent RNA-seq and liquid chromatography–mass spectrometry (LC-MS) analyses comparing extreme phenotypes identified 573 differentially expressed genes (DEGs) and 784 differentially accumulated metabolites (DAMs). Joint multi-omics analysis revealed 14 consistently enriched pathways, highlighting the crucial role of secondary metabolite biosynthesis. Notably, Glyma.19G030500, which encodes an isoflavone malonyltransferase, was identified as the primary hub gene. These findings offer valuable genomic targets for the marker-assisted breeding of soybean varieties with optimized processing qualities. Full article

Soybean (Glycine max L.) is an important agricultural crop for human food and animal feed. Soybean yield is severely constrained by abiotic stresses such as salinity and drought, which affect large proportions of arable and irrigated lands worldwide. This necessitates the development of new soybean varieties tolerant to these stress factors. Mutation breeding is an effective approach to improve the stress tolerance of plants due to increased genetic diversity. In this study, two gamma-induced salinity and drought-tolerant soybean mutants (SM1 and SM3-1) were compared with the parental line S04-05 using GO and KEGG pathway enrichment analyses. GO enrichment analyses revealed extensive differential gene expression in the mutant lines under stress conditions, with significant enrichment of pathways related to photosynthesis, hormone signaling, carbohydrate metabolism, and flavonoid and isoflavonoid biosynthesis. Genotype-specific analyses indicated that the SM3-1 mutant exhibited a dynamic regulatory response associated with maintaining the photosynthetic apparatus and chloroplast homeostasis under stress, whereas the SM1 mutant showed an adaptation strategy based on metabolite-mediated osmotic adjustment and ROS scavenging. Compared to the parental variety S04-05, the mutants showed distinct metabolic regulation in phenylpropanoid/isoflavone metabolism, with upregulation of many isoflavone biosynthesis genes under salinity, drought, and untreated conditions, indicating a key and sustained role of this pathway in stress tolerance. Most SNPs identified in the isoflavone biosynthesis pathway consist of moderate-impact and modifier variations. These findings suggest that gamma mutagenesis and subsequent selection processes allow for the development of novel genetic variants that operate through different physiological and metabolic mechanisms but exhibit similar levels of tolerance. In this respect, the study reveals that mutation breeding is a potentially sustainable and effective breeding strategy for increasing abiotic stress tolerance in soybeans. Full article

As an isoflavone metabolite with diverse physiological activities, the development of efficient and sustainable manufacturing technologies for (S)-equol holds significant importance. This study focuses on the semi-rational design of daidzein reductase (DZNR), the first key enzyme in the (S)-equol biotransformation pathway. Through multiple sequence alignment and three-dimensional structural analysis, two critical residues, Gly30 and Ala105, were identified in DZNR. A library of single and combinatorial mutants was constructed and screened, yielding the double variant DZNR30S+105S with substantially enhanced catalytic performance. In a whole-cell biocatalytic system, the recombinant E. coli (Escherichia coli) strain harboring this combinatorial mutant achieved a yield of 238.3 mg/L (S)-equol at a substrate concentration of 1 mM daidzein, demonstrating markedly improved catalytic efficiency. Upon increasing the daidzein concentration to 2 mM, the reaction reached equilibrium within 5 h, producing 384.6 mg/L (S)-equol, which highlights the mutant’s excellent potential for high-substrate-concentration applications. This study not only provides novel mechanistic insights into DZNR catalysis but also successfully establishes a DZNR variant with enhanced activity, offering an efficient biocatalytic component for the industrial-scale biomanufacturing of (S)-equol and thereby advancing the development of green biosynthesis technologies for this valuable compound. Full article

Background/Objectives: The global rise in multidrug-resistant Staphylococcus aureus (MDR-SA) threatens the efficacy of existing antibiotics and necessitates alternative antibacterial strategies. Plant-derived isoflavones represent a promising but underexplored source of novel antimicrobials. Biochanin A, isolated from Cajanus cajan seeds, exhibits antibacterial activity and may act via noncanonical mechanisms. This study elucidates the mechanism of action and safety profile of Biochanin A against MDR-SA using integrated experimental and computational approaches. Methods: Antibacterial activity was assessed by minimum inhibitory concentration (MIC) testing. Membrane integrity and morphological alterations were evaluated using flow cytometry and scanning electron microscopy (SEM), respectively. Target gene modulation was analyzed by qRT-PCR, while molecular interactions were examined through in silico docking. Cytotoxicity was evaluated in normal mammalian kidney, liver, and cardiac cells. Results: Biochanin A inhibited MDR-SA with an MIC80 of 64 µg/mL. Flow cytometry showed membrane disruption in 74.46 ± 13.19% of treated cells, and SEM revealed a 20% reduction in cell size (561.95 ± 21.99 nm). Biochanin A markedly downregulated femA (94%) and femB (67%), with minimal effect on femX (10%). Docking analyses supported preferential binding to FemA (−7.7 kcal/mol) and FemB (−7.5 kcal/mol) proteins. No cytotoxic effects were observed in normal mammalian cells. Conclusions: Biochanin A is a promising plant-derived antibacterial candidate against MDR-SA, targeting key cell wall biosynthesis genes while maintaining mammalian safety. These findings position Biochanin A as a viable lead for further biochemical, structural, and in vivo pharmacological validation, highlighting the translational potential of plant-derived isoflavones in combating antibiotic resistance. Full article

Soil salinisation has become one of the major abiotic stresses limiting crop growth in the world. To enhance soybean productivity on saline lands, understanding its salt-stress response and underlying mechanisms is necessary. In this study, the salt-tolerant soybean Kefeng 1 and the salt-sensitive soybean Qihuang 1 were used to elucidate the synergistic regulatory networks underlying soybean salt tolerance. After 12 days of 150 mM NaCl treatment, both varieties were subjected to phenotypic evaluation, physiological measurements, and integrated transcriptomic and metabolomic analysis. The results showed that the salt tolerance in Kefeng 1 primarily originated from its root. Under salt stress, Kefeng 1 maintained Na⁺/K⁺ ion homeostasis by up-regulating Cation/H⁺ Exchanger 15 (CHX15) and Cation Exchanger 3 (CAX3), and down-regulating Cyclic Nucleotide-Gated Channel 13 (CNGC13). Furthermore, Kefeng 1 stabilised auxin (IAA) homeostasis by inhibiting IAA biosynthesis and regulating concentrations through PIN-FORMED 3 (PIN3)-mediated efflux. It also scavenged reactive oxygen species (ROS) by employing enhanced enzymatic antioxidant systems, specifically aldo-keto reductase 1 (AKR1), glutathione S-transferase (GST), and catalase (CAT), alongside non-enzymatic antioxidants like the isoflavone genistein. Gene–metabolite correlation network analysis identified Glyma.09G117900 (PIN3) and Glyma.19G244200 (AKR1) as two hub genes. These two genes were specifically up-regulated in Kefeng 1 root under NaCl stress, and the proteins they encoded played important roles in salt tolerance in Kefeng 1 root as described above. Accordingly, these two genes were identified as candidate genes for salt tolerance in Kefeng 1. This study offered a theoretical framework and genetic resources for developing salt-tolerant soybean cultivars. Full article

(1) Background: This study used Qingjian No. 1 forage pea (Pisum sativum L.) as a plant material to study its metabolic mechanisms in response to different stresses, given that saline–alkali stress and drought stress often occur simultaneously in natural environments and severely affect the growth and yield of forage pea, while the regulatory network underlying the adaptation of forage pea to combined stress remains poorly elucidated. (2) Methods: The metabolic mechanisms of forage pea in response to different stresses were elucidated by integrating phenotypic, physiological, and metabolomic analyses. (3) Results: The results show that compared to the control, all stress treatments significantly inhibited seed germination and seedling growth, with the combined saline–alkali and drought stress exhibiting the strongest inhibitory effect. In terms of physiological and biochemical responses, peroxidase (POD) activity increased with the complexity of the stress, with the highest POD activity observed under combined saline–alkali and drought stress, showing a 61.71% increase compared to the control (p < 0.05). Non-targeted metabolomic analysis revealed that isoflavone biosynthesis, nucleotide metabolism, and cutin–suberin–wax biosynthesis are the core responsive pathways. Correlation analysis revealed that isocorydine and phosphatidylinositol phosphate showed strong positive correlations with the vigor index, main root length, and superoxide dismutase (SOD) activity, and glycerophospholipid metabolites were positively correlated with ferric ion-reducing antioxidant capacity. (4) This study deepens understanding of the stress resistance mechanisms in forage peas and provides a theoretical basis for stress-resistant forage pea breeding. Full article

Intestinal health is critical for nutrient absorption and disease resistance in cultured fish. Yet, the effects of dietary Eucalyptus-derived biochar on the gut of largemouth bass (Micropterus salmoides) remain largely unexplored. This study evaluated whether supplementing diets with Eucalyptus biochar c profiles. In a 56-day feeding trial, M. salmoides were offered a standard diet containing either 0% (control) or graded levels of biochar. Juvenile fish (initial body weight 13.34 g) were randomly distributed into six groups with three replicates each (30 fish per replicate). Six extruded diets were formulated with 0, 2.5, 5.0, 10.0, 20.0, or 40.0 g kg⁻¹ of biochar, designated G0 through G5. Biochar had no significant effects on villus length, muscle layer thickness, villus width, or the activities of trypsin, amylase, and lipase, though goblet cell number was significantly higher in G5. mRNA expression of Claudin-3 and IL-10 was significantly upregulated in G1–G4, while IL-1β was significantly downregulated in G4 and G5, and TNF-α expression was reduced in G2 and G3. 16S rDNA sequencing showed increasing trends in the relative abundance of Firmicutes (43% to 49.17%) and Lactococcus (0% to 1.10%) in G3, accompanied by decreases in Proteobacteria and Klebsiella. Metabolomic analysis indicated significant upregulation of taurochenodeoxycholic acid-7-sulfate, apigenin, genistein, baicalein, taurocholic acid-3-sulfate, taurochenodeoxycholic acid-3-sulfate, and arginylmethionine in G3, whereas etoxazole and soyasaponin were significantly reduced. Dietary inclusion of 10 g kg⁻¹ Eucalyptus biochar improved intestinal health in largemouth bass by shaping the gut microbiota, promoting isoflavone biosynthesis and bile acid and amino acid metabolism, inhibiting the NF-κB pathway, and reinforcing the intestinal barrier. Full article

High-fat diets are commonly used in eel aquaculture to reduce protein costs, but excessive fat intake can impair intestine health. This study investigated whether soy isoflavones (SIFs), an emulsifying additive, could mitigate the negative effects of high-fat diets in eel. Six hundred eels (30.00 g) were randomly divided into four groups with three replicates: control (CK, 5.96% fat), high-fat diet (HFD, 11.96% fat), and HFD supplemented with 50 mg/kg (LSF) or 100 mg/kg SIF (HSF) for 8 weeks. Results show that SIF supplementation reversed adverse effects on eels fed high-fat diets, reducing intestine damage (better villi development and lower malondialdehyde levels) and improving antioxidant capacity (higher glutathione, p < 0.05). SIFs also increased key antioxidant-related enzyme activities (catalase, superoxide dismutase, p < 0.05). Gut microbiota analysis revealed that SIFs restored microbial balance by reducing Proteobacteria (Pseudomonas) and increasing Firmicutes (Lactococcus), while suppressing harmful metabolic pathways like lipopolysaccharide biosynthesis. These findings demonstrate that dietary SIFs (50 mg/kg) effectively counteract high-fat diet-induced intestine damage and gut dysbiosis in eels, offering a practical nutritional strategy for sustainable aquaculture. Full article

Triclocarban (TCC), a synthetic antimicrobial compound prevalent in personal care products, has emerged as a typical contaminant in aquatic ecosystems. Intestinal microbiota maintains the host’s health homeostasis by regulating nutrient metabolism and immunity and is regarded as a sensitive biomarker for the risk assessment of pollutants. Currently, there is still a lack of toxicity assessment of TCC on the intestinal microbiota homeostasis of shrimp. Therefore, this study employed 16S rDNA sequencing to explore intestinal microbiota perturbations in Penaeus monodon following subchronic exposure (14 days) to graded TCC concentrations (1 and 10 μg/L). The results showed that TCC exposure altered intestinal microbiota diversity, marked by increases in the ACE, Chao1, and Shannon indices and a decrease in the Simpson index; however, none of these changes reached statistical significance (p > 0.05). Furthermore, the community composition was also altered, characterized by a significant increase in Bacteroidetes and a significant decrease in Tenericutes (p < 0.05), alongside non-significant increases in Proteobacteria and decreases in Firmicutes (p > 0.05). The abundances of some putative beneficial bacterial genera (Alloprevotella, Bacteroidales S24-7 group_norank, Cetobacterium, Enterococcus and Lactobacillus) and harmful bacteria (Photobacterium and Aeromonas) were decreased (p > 0.05); the abundance of Vibrio was decreased in the T1 group but increased in the T10 group (p > 0.05). Additionally, the predicted functions of the intestinal microbiota, such as glycan biosynthesis and degradation, steroid and isoflavone biosynthesis, and nucleotide metabolism, were enhanced. These results indicated that TCC exposure had a negative effect on the homeostasis of the intestinal microbiota of P. monodon. Full article

Isoflavone synthase (IFS) is the key enzyme in isoflavonoid biosynthesis and has been functionally characterized in numerous plant species. Glycyrrhiza species, valued for their medicinal properties, accumulate flavonoids with significant physiological activities. Among these, isoflavones play crucial roles in plant growth, development and stress responses. However, the IFS gene family in Glycyrrhiza remains poorly understood. In this study, we identified 10, 9 and 9 IFS genes in G. uralensis, G. inflata and G. glabra, respectively. Phylogenetic analysis classified these genes into four distinct clades (Clade A–D). Further characterization included chromosomal localization, gene structure, conserved motifs, cis-acting elements and synteny analysis. Using yeast one-hybrid (Y1H) screening, dual-luciferase assays and an electrophoretic mobility shift assay (EMSA), these results revealed that auxin response factor 4 (GgARF4) directly binds to the isoflavone synthase 9 (GgIFS9) promoter and activates its expression. Following indole-3-acetic acid (IAA) treatment, RNA-seq revealed that in the differentially expressed genes (DEGs), the genes involved in isoflavonoid and flavonoid biosynthesis pathways were significantly enriched. The result of quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that GgIFS9 was strongly induced by IAA. β-Glucuronidase (GUS) assays confirmed that IAA activates the expression of the GgIFS9 promoter in Nicotiana tabacum. Our findings reveal that, through GgARF4 and its downstream-activated gene GgIFS9, IAA may promote flavonoid synthesis in G. glabra. This study provides novel insights into the auxin-mediated regulation of secondary metabolism in Glycyrrhiza species. Full article

The pericarp of Macadamia integrifolia represents a promising but underexplored source of functional flavonoids. To systematically elucidate their biosynthesis and enhance the industrial potential of this by-product, we conducted integrated transcriptomic and metabolomic profiling of pericarps across five developmental stages (50, 80, 110, 140, and 170 days after flowering). Our analysis reveals, for the first time, a distinct temporal shift in both gene expression and metabolite accumulation. Early stages were characterized by high expression of PAL, 4CL, CHS, and FLS, coupled with abundant flavonols and anthocyanins. In contrast, late stages exhibited upregulation of CHI and F3’5’H, redirecting the metabolic flux toward flavanones and isoflavones. This dynamic profile was closely associated with jasmonate and gibberellin signaling pathways and was likely regulated by key transcription factors (MYB, NAC, bHLH). These findings provide a multi-omics framework that elucidates the temporal flavonoid biosynthesis in macadamia pericarp, thereby laying the groundwork for its future industrial valorization. Full article

Salt–alkaline soil poses a significant challenge to soybean productivity. While plant growth-promoting rhizobacteria (PGPR) offer a sustainable strategy for stress mitigation, their field-level application remains underexplored. Here, a field experiment was conducted in the Yellow River Delta of Shandong, China, a typical salt–alkaline region. In this study, we evaluated the effectiveness of Bacillus velezensis 41S2 in enhancing soybean performance under salt–alkaline soil through integrated field trials and transcriptomic analysis. Inoculation with strain 41S2 significantly improved plant biomass, yield components, and seed yield under salt–alkaline soil, and notably increased seed protein and isoflavone contents. Physiological analyses revealed that strain 41S2 markedly reduced hydrogen peroxide (H₂O₂) accumulation, indicating alleviation of oxidative stress. Moreover, strain 41S2 modulated the levels of soluble sugars and amino acids, contributing to osmotic regulation and carbon–nitrogen (C-N) metabolic balance. Transcriptome profiling further indicated that strain 41S2 upregulated genes involved in antioxidant response, C–N metabolism, and phenylpropanoid biosynthesis, highlighting its role in coordinating multilayered stress response pathways. Overall, these findings highlight the potential of B. velezensis 41S2 as a multifunctional bioinoculant for improving salt tolerance and presents a promising tool for sustainable crop production and ecological restoration in salt–alkaline soil. Full article

Domestication has been proven to significantly impact the biosynthesis of plant secondary metabolites. Cultivated green jujube (Ziziphus mauritiana Lam.), as an important autotetraploid fruit crop widely planted in tropical regions, exhibits differential physicochemical traits compared with its wild progenitor. To assess the traits lost in cultivated green jujube during domestication, the study performed comprehensive genomic, transcriptomic and metabolomic investigations of flavonoid pathways in wild and cultivated green jujube. Based on the four haplotype genomes of wild and cultivated green jujube, for the first time, the study bulk-identified 16 key gene families associated with flavonoid biosynthesis. Collinearity analysis revealed that tandem duplication was the predominant event in flavonoid-related genes rather than WGD. Through the expression profiles in different tissues, the distinct member of these gene families was classified as “redundant” or “functional”. Transcriptomic analyses illustrated the significant differential expressions (p < 0.05) of 13 flavonoid-related gene families in fruits of six cultivated and three wild green jujube accessions, except for FLS, LAR and PPO. The wild green jujube fruits accumulated more abundance of flavonoid metabolites than in cultivated fruits (p < 0.0001), as evidenced by upregulated chalcones, dihydroflavonol, isoflavones and flavonoid carbonoside. Gene–metabolite co-expression modules further validated the potential transcription regulators, such as BBX21, WRI1 and bZIP44. Together, the study suggested a genomic, transcriptomic and metabolic perspective for domestication regarding fruit flavonoid pathways in green jujube, which provides a valuable genetic resource for fruit quality improvement in cultivated green jujube. Full article

This study investigates how root color in soybeans affects isoflavone composition, rhizosphere bacterial diversity, total phenolics, total flavonoids, and antioxidant activity under a hydroponic cultivation system. Notably, soybean-brown roots (SBRs) accumulated significantly higher contents of isoflavones, exhibiting approximately a 14.9-fold increase in total glycosides (141.75 to 2121.59 µg/g), 7.3-fold increase in total malonyl-β-glycosides (127.52 to 930.45 µg/g), 2.8-fold increase in total aglycones (1825.90 to 5145.21 µg/g), and 3.9-fold increase in total isoflavones (2095.16 to 8197.26 µg/g) than soybean-white roots (SWRs). Isolated rhizosphere bacteria profiling revealed γ-Proteobacteria as the predominant class in both root types, constituting 77.6% and 73.9% of the bacterial community in SWRs and SBRs, respectively. However, SBRs supported a more diverse bacterial ecosystem, harboring thirteen genera compared to only eight genera in SWRs. Enhanced total phenolics, total flavonoids, and radical scavenging activity were also associated with the SBRs. These findings shed light on the dynamic interplay between root traits, bacterial interactions, and secondary metabolite biosynthesis in hydroponically grown soybeans. This work not only advances our understanding of plant root–microbiome–metabolite relationships but also offers a novel approach to exploring the potential of enhancing secondary metabolites in soybean plants through precision cultivation. Full article

Flavonoids are a class of secondary metabolites synthesized by plants, characterized by a C6-C3-C6 carbon skeleton and derived from the phenylpropane metabolism pathway. They play crucial biological roles, not only in plant pigment production and responses to biotic and abiotic stresses but also in medicinal applications. Consequently, the biosynthesis and regulatory mechanisms of flavonoids have been a focal point in plant transcription and gene expression research. The biosynthetic pathways of flavonoids include branches such as isoflavones, flavones, flavonols, anthocyanins, and proanthocyanidins, with some pathways and key enzymes already well-characterized. Studies indicate that plant flavonoids are regulated by various factors, including transcription factors, non-coding endogenous small RNAs (miRNAs), and plant hormones. This review systematically summarizes the structure and classification of plant flavonoids, their biosynthetic and regulatory mechanisms, and the factors influencing flavonoid synthesis. By discussing the regulation of flavonoid-related gene expression in plants, this work provides valuable insights and a theoretical foundation for future research and applications of flavonoids. Full article