Elucidating the role of exogenous melatonin in mitigating alkaline stress in soybeans across different growth stages: a transcriptomic and metabolomic approach.

BACKGROUND: Soybean (Glycine max), a vital grain and oilseed crop, serves as a primary source of plant protein and oil. Soil salinization poses a significant threat to soybean planting, highlighting the urgency to improve soybean resilience and adaptability to saline stress. Melatonin, recently identified as a key plant growth regulator, plays crucial roles in plant growth, development, and responses to environmental stress. However, the potential of melatonin to mitigate alkali stress in soybeans and the underlying mechanisms remain unclear. RESULTS: This study investigated the effects of exogenous melatonin on the soybean cultivar Zhonghuang 13 under alkaline stress. We employed physiological, biochemical, transcriptomic, and metabolomic analyses throughout both vegetative and pod-filling growth stages. Our findings demonstrate that melatonin significantly counteracts the detrimental effects of alkaline stress on soybean plants, promoting plant growth, photosynthesis, and antioxidant capacity. Transcriptomic analysis during both growth stages under alkaline stress, with and without melatonin treatment, identified 2,834 and 549 differentially expressed genes, respectively. These genes may play a vital role in regulating plant adaptation to abiotic stress. Notably, analysis of phytohormone biosynthesis pathways revealed altered expression of key genes, particularly in the ARF (auxin response factor), AUX/IAA (auxin/indole-3-acetic acid), and GH3 (Gretchen Hagen 3) families, during the early stress response. Metabolomic analysis during the pod-filling stage identified highly expressed metabolites responding to melatonin application, such as uteolin-7-O-(2''-O-rhamnosyl)rutinoside and Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside, which helped alleviate the damage caused by alkali stress. Furthermore, we identified 183 differentially expressed transcription factors, potentially playing a critical role in regulating plant adaptation to abiotic stress. Among these, the gene SoyZH13_04G073701 is particularly noteworthy as it regulates the key differentially expressed metabolite, the terpene metabolite Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside. WGCNA analysis identified this gene (SoyZH13_04G073701) as a hub gene, positively regulating the crucial differentially expressed metabolite of terpenoids, Hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)glucoside. Our findings provide novel insights into how exogenous melatonin alleviates alkali stress in soybeans at different reproductive stages. CONCLUSIONS: Integrating transcriptomic and metabolomic approaches, our study elucidates the mechanisms by which exogenous melatonin ameliorates the inhibitory effects of alkaline stress on soybean growth and development. This occurs through modulation of biosynthesis pathways for key compounds, including terpenes, flavonoids, and phenolics. Our findings provide initial mechanistic insights into how melatonin mitigates alkaline stress in soybeans, offering a foundation for molecular breeding strategies to enhance salt-alkali tolerance in this crop.

Complexes of soybean protein fibrils and chlorogenic acid: Interaction mechanism and antibacterial activity.

This study explored the mechanism of interaction between chlorogenic acid (CA) and protein fibrils (PF) as well as the effects of varying the CA/PF concentration ratio on antibacterial activity. Analysis of various parameters, such as ζ-potential, thioflavin T fluorescence intensity, surface hydrophobicity, and free sulfhydryl groups, revealed that the interaction between PF and CA altered the structure of PF. Fluorescence analysis revealed that hydrogen bonding and hydrophobic interactions were the primary interaction forces causing conformational rearrangement, resulting in a shorter, more flexible, and thicker fibril structure, as observed through transmission electron microscopy. Fourier-transform infrared spectroscopy, small-angle X-ray scattering, and X-ray diffraction analyses revealed that the characteristic fibril structure was destroyed when the CA/PF ratio exceeded 0.05. Notably, the CA-PF complexes inhibited the growth of Escherichia coli and Staphylococcus aureus and also exhibited antioxidant activity. Overall, this study expands the application prospects of CA and PF in the food industry.

Soybean isolate protein complexes with different concentrations of inulin by ultrasound treatment: Structural and functional properties.

The effects of ultrasound and different inulin (INU) concentrations (0, 10, 20, 30, and 40 mg/mL) on the structural and functional properties of soybean isolate protein (SPI)-INU complexes were hereby investigated. Fourier transform infrared spectroscopy showed that SPI was bound to INU via hydrogen bonding. All samples showed a decreasing and then increasing trend of α-helix content with increasing INU concentration. SPI-INU complexes by ultrasound with an INU concentration of 20 mg/mL (U-2) had the lowest content of α-helix, the highest content of random coils and the greatest flexibility, indicating the proteins were most tightly bound to INU in U-2. Both UV spectroscopy and intrinsic fluorescence spectroscopy indicated that it was hydrophobic interactions between INU and SPI. The addition of INU prevented the exposure of tryptophan and tyrosine residues to form a more compact tertiary structure compared to SPI alone, and ultrasound caused further unfolding of the structure of SPI. This indicated that the combined effect of ultrasound and INU concentration significantly altered the tertiary structure of SPI. SDS-PAGE and Native-PAGE displayed the formation of complexes through non-covalent interactions between SPI and INU. The ζ-potential and particle size of U-2 were minimized to as low as -34.94 mV and 110 nm, respectively. Additionally, the flexibility, free sulfhydryl groups, solubility, emulsifying and foaming properties of the samples were improved, with the best results for U-2, respectively 0.25, 3.51 µmoL/g, 55.51 %, 269.91 %, 25.90 %, 137.66 % and 136.33 %. Overall, this work provides a theoretical basis for improving the functional properties of plant proteins.

Dissecting the Genetic Basis of Yield Traits and Validation of a Novel Quantitative Trait Locus for Grain Width and Weight in Rice.

Grain yield in rice is a complex trait and it is controlled by a number of quantitative trait loci (QTL). To dissect the genetic basis of rice yield, QTL analysis for nine yield traits was performed using an F2 population containing 190 plants, which was developed from a cross between Youyidao (YYD) and Sanfenhe (SFH), and each plant in the population evaluated with respect to nine yield traits. In this study, the correlations among the nine yield traits were analyzed. The grain yield per plant positively correlated with six yield traits, except for grain length and grain width, and showed the highest correlation coefficient of 0.98 with the number of filled grains per plant. A genetic map containing 133 DNA markers was constructed and it spanned 1831.7 cM throughout 12 chromosomes. A total of 36 QTLs for the yield traits were detected on nine chromosomes, except for the remaining chromosomes 5, 8, and 9. The phenotypic variation was explained by a single QTL that ranged from 6.19% to 36.01%. Furthermore, a major QTL for grain width and weight, qGW2-1, was confirmed to be newly identified and was narrowed down to a relatively smaller interval of about ~2.94-Mb. Collectively, we detected a total of 36 QTLs for yield traits and a major QTL, qGW2-1, was confirmed to control grain weight and width, which laid the foundation for further map-based cloning and molecular design breeding in rice.

Fine Mapping of qAL5.2 Controlling Anther Length in Oryza sativa.

Anther length is the critical floral trait determining hybrid rice seed production and is controlled by many quantitative trait loci (QTL). However, the cloning of genes specifically controlling anther size has yet to be reported. Here, we report the fine mapping of qAL5.2 for anther size using backcross inbred lines (BILs) in the genetic background of Oryza sativa indica Huazhan (HZ). Gene chip analysis on the BC4F2 and BC5F1 population identified effective loci on Chr1, Chr5, and Chr8 and two genomic regions on Chr5, named qAL5.1 and qAL5.2. qAL5.2 was identified in both populations with LOD values of 17.54 and 10.19, which explained 35.73% and 25.1% of the phenotypic variances, respectively. Ultimately qAL5.2 was localized to a 73 kb region between HK139 and HK140 on chromosome 5. And we constructed two near-isogenic lines (NILs) for RNA-seq analysis, named NIL-qAL5.2HZ and NIL-qAL5.2KLY, respectively. The result of the GO enrichment analysis revealed that differential genes were significantly enriched in the carbohydrate metabolic process, extracellular region, and nucleic acid binding transcription, and KEGG enrichment analysis revealed that alpha-linolenic acid metabolism was significantly enriched. Meanwhile, candidate genes of qAL5.2 were analyzed in RNA-seq, and it was found that ORF8 is differentially expressed between NIL-qAL5.2HZ and NIL-qAL5.2KLY. The fine mapping of qAL5.2 conferring anther length will promote the breed improvement of the restorer line and understanding of the mechanisms driving crop mating patterns.

Liposomes decorated with ß-conglycinin and glycinin: Construction, structure and in vitro digestive stability.

Liposomes were modified with different proportions of ß-conglycinin (7S) and glycinin (11S) to form Lip-7S and Lip-11S. The morphology, interaction and in vitro simulated digestion of liposomes were studied. The particle size of Lip-7S was smaller than that of Lip-11S. When the values of Lip-7S and Lip-11S were 1:1 and 1:0.75, respectively, the ζ-potential had the maximum absolute value and the dispersion of the system was good. The results of multispectral analysis showed that hydrogen-bond and hydrophobic interaction dominated protein-modified liposomes, the protein structure adsorbed on the surface of liposomes changed, the content of α-helix decreased, and the structure of protein-modified liposomes became denser. The surface hydrophobicity and micropolarity of liposomes decreased with the increase of protein ratio, and tended to be stable after Lip-7S (1:1) and Lip-11S (1:0.75). Differential scanning calorimetry showed that Lip-7S had higher phase transition temperature (≥170.5 °C) and better rigid structure. During simulated digestion, Lip-7S (22.5 %) released less Morin than Lip (40.6 %) and Lip-11S (26.2 %), and effectively delayed the release of FFAs. The environmental stability of liposomes was effectively improved by protein modification, and 7S had better modification effect than 11S. This provides a theoretical basis for 7S and 11S modified liposomes, and also provides a data reference for searching for new materials for stabilization of liposomes.

Impact of soybean protein isolate concentration on chitosan-cellulose nanofiber edible films: Focus on structure and properties.

Chitosan and cellulose nanofiber films are frequently employed as biodegradable materials for food packaging. However, many exhibit suboptimal hydrophobicity and antioxidant properties. To address these shortcomings, we enhanced the performance by adding different concentrations of soybean protein isolate (SPI) to chitosan-cellulose nanofiber (CS-CNF) films. As SPI concentration varied, the turbidity, particle size, and ζ-potential of the film-forming solutions initially decreased and subsequently increased. This suggests that 1 % SPI augments the electrostatic attraction and compatibility. Rheological analysis confirmed a pronounced apparent viscosity at this concentration. Analyses using Fourier transform infrared spectra, Raman spectra, X-ray diffraction, and Scanning electron microscope revealed the presence of hydrogen bonds and electrostatic interactions between SPI and CS-CNF, indicative of superior compatibility. When SPI concentration was set at 1 %, notable enhancements in film attributes were observed: improvements in tensile strength and elongation at break, a reduction in water vapor permeability by 8.23 %, and an elevation in the contact angle by 18.85 %. Furthermore, at this concentration, the ABTS+ and DPPH scavenging capacities of the film surged by 61.53 % and 46.18 %, respectively. Meanwhile, the films we prepare are not toxic. This research offers valuable insights for the advancement and application of protein-polysaccharide-based films.

Effects of sucrase enzymatic hydrolysis combined with Maillard reaction on soy protein hydrolysates: Bitterness and functional properties.

In this study, sucrase was added to convert non-reducing sugars into reducing sugars in skim obtained by enzyme-assisted aqueous extraction processing (EAEP), then the variation of soy protein hydrolysates (SPH) from the skim under different Maillard reaction times were studied. We conducted one-factor experiment and selected 2 mg/mL sucrase for enzymatic hydrolysis for 2 h. The structure of SPH was investigated by Fourier transform infrared spectroscopy, intrinsic fluorescence spectroscopy, and amino acid composition. Results showed that the Maillard reaction loosened the SPH structure and produced new functional groups. Sensory evaluation, electronic tongue, electronic nose and GC-MS were used to study the sensory characteristics of SPH, we found that the bitterness value was significantly reduced to 1.71 from 4.63 after 2 h of the Maillard reaction. The change of bitterness was related to amino acid composition and the production of pyrazine. Additionally, the iron reduction ability, DPPH free radical scavenging ability, and emulsifying activity reached the highest at 2 h of reaction with 0.80, 73.94 %, and 56.09 %. The solubility, emulsifying stability, and foaming capacity increased and gradually stabilized with the increasing reaction time. Therefore, this paper presents an effective method for generating SPH with low bitterness and high functional properties.

Physiological responses and transcriptome analysis of soybean under gradual water deficit.

Soybean is an important food and oil crop widely cultivated globally. However, water deficit can seriously affect the yield and quality of soybeans. In order to ensure the stability and increase of soybean yield and improve agricultural water use efficiency (WUE), research on improving drought tolerance and the efficiency of water utilization of soybeans under drought stress has become particularly important. This study utilized the drought-tolerant variety Heinong 44 (HN44) and the drought-sensitive variety Suinong 14 (SN14) to analyze physiological responses and transcriptome changes during the gradual water deficit at the early seed-filling stage. The results indicated that under drought conditions, HN44 had smaller stomata, higher stomatal density, and lower stomatal conductance (Gs) and transpiration rate as compared to SN14. Additionally, HN44 had a higher abscisic acid (ABA) content and faster changes in stomatal morphology and Gs to maintain a dynamic balance between net photosynthetic rate (Pn) and Gs. Additionally, drought-tolerant variety HN44 had high instantaneous WUE under water deficit. Further, HN44 retained a high level of superoxide dismutase (SOD) activity and proline content, mitigating malondialdehyde (MDA) accumulation and drought-induced damage. Comprehensive analysis of transcriptome data revealed that HN44 had fewer differentially expressed genes (DEGs) under light drought stress, reacting insensitivity to water deficit. At the initial stage of drought stress, both varieties had a large number of upregulated DEGs to cope with the drought stress. Under severe drought stress, HN44 had fewer downregulated genes enriched in the photosynthesis pathway than SN14, while it had more upregulated genes enriched in the ABA-mediated signaling and glutathione metabolism pathways than SN14. During gradual water deficit, HN44 demonstrated better drought-tolerant physiological characteristics and water use efficiency than SN14 through key DEGs such as GmbZIP4, LOC100810474, and LOC100819313 in the major pathways. Key transcription factors were screened and identified, providing further clarity on the molecular regulatory pathways responsible for the physiological differences in drought tolerance among these varieties. This study deepened the understanding of the drought resistance mechanisms in soybeans, providing valuable references for drought-resistant soybean breeding.

Genome Survey and Chromosome-Level Draft Genome Assembly of Glycine max var. Dongfudou 3: Insights into Genome Characteristics and Protein Deficiencies.

Dongfudou 3 is a highly sought-after soybean variety due to its lack of beany flavor. To support molecular breeding efforts, we conducted a genomic survey using next-generation sequencing. We determined the genome size, complexity, and characteristics of Dongfudou 3. Furthermore, we constructed a chromosome-level draft genome and speculated on the molecular basis of protein deficiency in GmLOX1, GmLOX2, and GmLOX3. These findings set the stage for high-quality genome analysis using third-generation sequencing. The estimated genome size is approximately 1.07 Gb, with repetitive sequences accounting for 72.50%. The genome is homozygous and devoid of microbial contamination. The draft genome consists of 916.00 Mb anchored onto 20 chromosomes, with annotations of 46,446 genes and 77,391 transcripts, achieving Benchmarking Single-Copy Orthologue (BUSCO) completeness of 99.5% for genome completeness and 99.1% for annotation. Deletions and substitutions were identified in the three GmLox genes, and they also lack corresponding active proteins. Our proposed approach, involving k-mer analysis after filtering out organellar DNA sequences, is applicable to genome surveys of all plant species, allowing for accurate assessments of size and complexity. Moreover, the process of constructing chromosome-level draft genomes using closely related reference genomes offers cost-effective access to valuable information, maximizing data utilization.

ABF1 Positively Regulates Rice Chilling Tolerance via Inducing Trehalose Biosynthesis.

Chilling stress seriously limits grain yield and quality worldwide. However, the genes and the underlying mechanisms that respond to chilling stress remain elusive. This study identified ABF1, a cold-induced transcription factor of the bZIP family. Disruption of ABF1 impaired chilling tolerance with increased ion leakage and reduced proline contents, while ABF1 over-expression lines exhibited the opposite tendency, suggesting that ABF1 positively regulated chilling tolerance in rice. Moreover, SnRK2 protein kinase SAPK10 could phosphorylate ABF1, and strengthen the DNA-binding ability of ABF1 to the G-box cis-element of the promoter of TPS2, a positive regulator of trehalose biosynthesis, consequently elevating the TPS2 transcription and the endogenous trehalose contents. Meanwhile, applying exogenous trehalose enhanced the chilling tolerance of abf1 mutant lines. In summary, this study provides a novel pathway 'SAPK10-ABF1-TPS2' involved in rice chilling tolerance through regulating trehalose homeostasis.

Exogenous abscisic acid represses rice flowering via SAPK8-ABF1-Ehd1/Ehd2 pathway.

INTRODUCTION: Rice flowering is a major agronomic trait, determining yield and ecological adaptability in particular regions. ABA plays an essential role in rice flowering, but the underlying molecular mechanism remains largely elusive. OBJECTIVES: In this study, we demonstrated a "SAPK8-ABF1-Ehd1/Ehd2" pathway, through which exogenous ABA represses rice flowering in a photoperiod-independent manner. METHODS: We generated abf1 and sapk8 mutants using the CRISPR-Cas9 method. Using yeast two-hybrid, Pull down, BiFC and kinase assays, SAPK8 interacted and phosphorylated ABF1. ABF1 directly bound to the promoters of Ehd1 and Ehd2 using ChIP-qPCR, EMSA, and LUC transient transcriptional activity assay, and suppressed the transcription of these genes. RESULTS: Under both long day and short day conditions, simultaneous knock-out of ABF1 and its homolog bZIP40 accelerated flowering, while SAPK8 and ABF1 over-expression lines exhibited delayed flowering and hypersensitivity to ABA-mediated flowering repression. After perceiving the ABA signal, SAPK8 physically binds to and phosphorylates ABF1 to enhance its binding to the promoters of master positive flowering regulators Ehd1 and Ehd2. Upon interacting with FIE2, ABF1 recruited PRC2 complex to deposit H3K27me3 suppressive histone modification on Ehd1 and Ehd2 to suppress these genes transcription, thereby leading to later flowering. CONCLUSION: Our work highlighted the biological functions of SAPK8 and ABF1 in ABA signaling, flowering control and the involvement of a PRC2-mediated epigenetic repression mechanism in the transcription regulation governed by ABF1 on ABA-mediated rice flowering repression.

pH-Shifting combined with ultrasound treatment of emulsion-filled ß-conglycinin gels as ß-carotene carriers: Effect of emulsion concentration on gel properties.

In this work, emulsion-filled gels were prepared from natural and pH-shifting combined with ultrasound ß-conglycinin (7S) as emulsifiers. The emulsifier modification and emulsion concentrations (5, 10, 15, 20 wt%) were evaluated on the structural and ß-carotene release properties of the gels. Compared to the 7S hydrogel, the emulsion-filled gels exhibited better water-holding and textural properties. The 7S modification and the increase in emulsion concentration resulted in altered water distribution and improved microstructure and rheological properties of the emulsion-filled gels. The dense and homogeneous gel network was formed at an emulsion content of 15 wt%. The gels were regulated by different release kinetics in a simulated gastrointestinal environment. M-15 showed the highest bioaccessibility and chemical stability (72.25% and 89.87%) with good slow-release properties of ß-carotene. These results will guide the development of encapsulated delivery systems for gel food products.

Microbial Diversity and Flavor Regularity of Soy Milk Fermented Using Kombucha.

Plant-based milk is considered a healthy and environmentally sustainable option. However, due to the low protein content of most plant-based milk and the difficulty of gaining flavor acceptance by consumers, its production scale is usually limited. Soy milk is a kind of food with comprehensive nutrition and high protein content. In addition, kombucha is naturally fermented by acetic acid bacteria (AAB), yeast, lactic acid bacteria (LAB), and other microorganisms, and the microorganisms in its system can improve the flavor characteristics of food. In the present study, LAB (commercially purchased) and kombucha were used as fermenting agents for soybean, which was used as a raw material to produce soy milk. A variety of characterization methods were used to study the relationship between the microbial composition and flavor regularity of soy milk produced with different proportions of fermenting agents and different fermentation times. In soy milk produced at 32 °C with a mass ratio of LAB to kombucha of 1:1 and a fermentation time of 42 h, the concentrations of LAB, yeast, and acetic acid bacteria in the milk were optimal at 7.48, 6.68, and 6.83 log CFU/mL, respectively. In fermented soy milk produced with kombucha and LAB, the dominant bacterial genera were Lactobacillus (41.58%) and Acetobacter (42.39%), while the dominant fungal genera were Zygosaccharomyces (38.89%) and Saccharomyces (35.86%). After 42 h, the content of hexanol in the fermentation system of kombucha and LAB decreased from 30.16% to 8.74%, while flavor substances such as 2,5-dimethylbenzaldehyde and linalool were produced. Soy milk fermented with kombucha offers the opportunity to explore the mechanisms associated with flavor formation in multi-strain co-fermentation systems and to develop commercial plant-based fermentation products.

Molecular structural modification of ß-conglycinin using pH-shifting with ultrasound to improve emulsifying properties and stability.

This present work underlines the effect of pH-shifting at pH 2 and pH 12 individually or combined with ultrasound treatment to modify the molecular structure of ß-conglycinin (7S) on its emulsifying properties and stability. Fourier transform infrared (FTIR) spectroscopy and intrinsic fluorescence spectroscopy showed that pH-shifting improves the molecular structure of 7S, while ultrasound further promotes structural changes. In particular, the pH-shifting at pH 12 combined with ultrasound treatment (U-7S-12) resulted in more significant changes than the pH-shifting at pH 2 combined with ultrasound (U-7S-2). U-7S-12 showed a significant reduction in protein particle size from 152 to 34.77 nm and a relatively smooth protein surface compared to 7S. The protein had the highest surface hydrophobicity and flexibility at 81,560.0 and 0.45, respectively, and the free sulfhydryl content from 1.57 to 2.02 µmol/g. In addition, we characterized the emulsions prepared after 7S treatment. The single or combined treatment increased the interfacial protein adsorption of the samples, which showed lower viscosity and shear stress compared to 7S. The U-7S-12 emulsion exhibited the highest emulsifying properties and was more stable than other emulsions under creaming, heating, and freeze-thaw conditions. In summary, the concerted action of pH-shifting and ultrasound can modify the structure, and combined alkaline pH-shifting and ultrasound treatment can further improve the emulsifying properties and stability of 7S.

New progress in diagnosis and treatment of pulmonary arterial hypertension.

Pulmonary arterial hypertension (PAH) is a progressive disease. Although great progress has been made in its diagnosis and treatment in recent years, its mortality rate is still very significant. The pathophysiology and pathogenesis of PAH are complex and involve endothelial dysfunction, chronic inflammation, smooth muscle cell proliferation, pulmonary arteriole occlusion, antiapoptosis and pulmonary vascular remodeling. These factors will accelerate the progression of the disease, leading to poor prognosis. Therefore, accurate etiological diagnosis, treatment and prognosis judgment are particularly important. Here, we systematically review the pathophysiology, diagnosis, genetics, prognosis and treatment of PAH.

Five Rice Seed-Specific NF-YC Genes Redundantly Regulate Grain Quality and Seed Germination via Interfering Gibberellin Pathway.

NF-YCs are important transcription factors with diverse functions in the plant kingdoms including seed development. NF-YC8, 9, 10, 11 and 12 are close homologs with similar seed-specific expression patterns. Despite the fact that some of the NF-YCs are functionally known; their biological roles have not been systematically explored yet, given the potential functional redundancy. In this study, we generated pentuple mutant pnfyc of NF-YC8-12 and revealed their functions in the regulation of grain quality and seed germination. pnfyc grains displayed significantly more chalkiness with abnormal starch granule packaging. pnfyc seed germination and post-germination growth are much slower than the wild-type NIP, largely owing to the GA-deficiency as exogenous GA was able to fully recover the germination phenotype. The RNA-seq experiment identified a total of 469 differentially expressed genes, and several GA-, ABA- and grain quality control-related genes might be transcriptionally regulated by the five NF-YCs, as revealed by qRT-PCR analysis. The results demonstrated the redundant functions of NF-YC8-12 in regulating GA pathways that underpin rice grain quality and seed germination, and shed a novel light on the functions of the seed-specific NF-YCs.