Search Results (153)

Pear (Pyrus pyrifolia) is an important deciduous fruit tree that requires a specific period of low-temperature accumulation to trigger spring flowering. The warmer winter caused by global warming has led to insufficient winter chilling, disrupting floral initiation and significantly reducing pear yields in Southern China. In this study, we integrated targeted phytohormone metabolomics, full-length transcriptomics, and proteomics to explore the regulatory mechanisms of dormancy in ‘Mixue’, a pear cultivar with an extremely low chilling requirement. Comparative analyses across the multi-omics datasets revealed 30 differentially abundant phytohormone metabolites (DPMs), 2597 differentially expressed proteins (DEPs), and 7722 differentially expressed genes (DEGs). Integrated proteomic and transcriptomic expression clustering analysis identified five members of the dormancy-associated MADS-box (DAM) gene family among dormancy-specific differentially expressed proteins (DEPs) and differentially expressed genes (DEGs). Phytohormone correlation analysis and cis-regulatory element analysis suggest that DAM genes may mediate dormancy progression by responding to abscisic acid (ABA), gibberellin (GA), and salicylic acid (SA). A dormancy-associated transcriptional regulatory network centered on DAM genes and phytohormone signaling revealed 35 transcription factors (TFs): 19 TFs appear to directly regulate the expression of DAM genes, 18 TFs are transcriptionally regulated by DAM genes, and two TFs exhibit bidirectional regulatory interactions with DAM. Within this regulatory network, we identified a novel pathway involving REVEILLE 6 (RVE6), DAM, and CONSTANS-LIKE 8 (COL8), which might play a critical role in regulating bud dormancy in the ‘Mixue’ low-chilling pear cultivar. Furthermore, lncRNAs ONT.19912.1 and ONT.20662.7 exhibit potential cis-regulatory interactions with DAM1/2/3. This study expands the DAM-mediated transcriptional regulatory network associated with bud dormancy, providing new insights into its molecular regulatory mechanisms in pear and establishing a theoretical framework for future investigations into bud dormancy control. Full article

Drought stress is an important abiotic stress factor restricting crop production. Broomcorn millet (Panicum miliaceum L.) has become an ideal material for analyzing the stress adaptation mechanisms of crops due to its strong stress resistance. However, the functional characteristics of its rhizosphere microorganisms in response to drought remain unclear. In this study, metagenomics and metabolomics techniques were employed to systematically analyze the compositional characteristics of the microbial community, functional properties, and changes in metabolites in the rhizosphere soil of broomcorn millet under drought stress. On this basis, an analysis was conducted in combination with the differences in functional pathways. The results showed that the drought treatment during the flowering stage significantly altered the species composition of the rhizosphere microorganisms of broomcorn millet. Among them, the relative abundances of beneficial microorganisms such as Nitrosospira, Coniochaeta, Diversispora, Gigaspora, Glomus, and Rhizophagus increased significantly. Drought stress significantly affects the metabolic pathways of rhizosphere microorganisms. The relative abundances of genes associated with prokaryotes, glycolysis/gluconeogenesis, and other metabolic process (e.g., ribosome biosynthesis, amino sugar and nucleotide sugar metabolism, and fructose and mannose metabolism) increased significantly. Additionally, the expression levels of functional genes involved in the phosphorus cycle were markedly upregulated. Drought stress also significantly alters the content of specific rhizosphere soil metabolites (e.g., trehalose, proline). Under drought conditions, broomcorn millet may stabilize the rhizosphere microbial community by inducing its restructuring and recruiting beneficial fungal groups. These community-level changes can enhance element cycling efficiency, optimize symbiotic interactions between broomcorn millet and rhizosphere microorganisms, and ultimately improve the crop’s drought adaptability. Furthermore, the soil metabolome (e.g., trehalose and proline) functions as a pivotal interfacial mediator, orchestrating the interaction network between broomcorn millet and rhizosphere microorganisms, thereby enhancing plant stress tolerance. This study sheds new light on the functional traits of rhizosphere microbiota under drought stress and their mechanistic interactions with host plants. Full article

Drought stress is one of the primary environmental factors affecting plant survival rates and productivity, and it is a key bottleneck restricting the development of the world kiwifruit industry. Therefore, studying the drought resistance-related genes and drought resistance mechanisms of kiwifruit is essential. The bHLH (basic helix-loop-helix) TF family plays a crucial role in the resistance of kiwifruit to abiotic stresses such as drought stress. In this study, we analyzed the response of the AcbHLH gene in kiwifruit under drought stress based on the kiwifruit genome database, transcriptome data, and metabolome data. One hundred eighty-seven AcbHLH genes were identified via bioinformatics and divided into eighteen subfamilies via phylogenetic analysis. The cis-acting elements of the AcbHLH gene are mainly hormone-related cis-acting elements. Under drought stress, 64 AcbHLH genes were significantly different, 5 AcbHLH genes whose expression significantly differed were randomly selected for qRT-PCR verification, and the correlation between the qRT-PCR results and the transcriptome data was high. The determination of plant hormone contents revealed that the contents of plant hormones, such as JA, changed markedly before and after drought stress. Through the combined analysis of transcriptome and metabolome data, it was speculated that AcbHLH84 and AcbHLH97 have functions similar to those of the MYC2 transcription factor and are the main downstream effectors in the JA signaling pathway; these functions could be activated and participate in the JA signaling pathway and that the activation of the JA signaling pathway would inhibit the production of reactive oxygen species. In turn, the drought resistance of kiwifruit is improved. The AcbHLH84 and AcbHLH97 genes could be candidate genes for breeding new transgenic drought-resistant kiwifruit varieties. Full article

Phosphorus (P), as one of the essential bulk elements for plant growth and development, plays an important role in root growth, accumulation of secondary metabolites, and regulation of gene expression. In Salvia miltiorrhiza Bunge (S. miltiorrhiza), an important medicinal plant, the accumulation of its active components is closely related to the level of phosphorus supply, but the molecular regulatory mechanism of phosphorus treatment in the growth and secondary metabolism of S. miltiorrhiza is not clear. In this study, we investigated the effects of low phosphorus (P2), moderate phosphorus (P4), and high phosphorus (P6) treatment on the growth and development of S. miltiorrhiza. seedlings, the accumulation of bioactive compounds, and their transcriptional regulation using transcriptomic and metabolomic analyses, and identified the key regulatory genes in the biosynthesis pathways of tanshinone and salvianolic acid. The findings revealed that S. miltiorrhiza biomass exhibited a “peaked” response to phosphorus concentration, peaking at 0.625 mmol·L⁻¹. At this optimal concentration, all four batches achieved maximum root length, root weight, and leaf weight: Batch I (11.3 cm, 2.34 g, 1.62 g), Batch II (12.7 cm, 2.67 g, 1.89 g), Batch III (13.8 cm, 2.85 g, 2.04 g), and Batch IV (15.6 cm, 3.51 g, 2.44 g). Both lower and higher concentrations resulted in growth inhibition and reduced bioactive compound accumulation. Transcription factors associated with root growth and development included bHLH, MYB, and WRKY; in particular, the bZIP23 transcription factor was highly expressed under abnormal phosphorus supply conditions. In addition, the biosynthetic pathways of tanshinone and salvianolic acid were elucidated, and key genes related to the synthesis pathways (CPS, KSL, CYP, PAL, HPPR, and RAS) were identified. The expression of several TFs (such as SmCPS1, SmCYP76AH3, SmCYP76AH1, SmGGPPS1, and SmRAS1) was found to be correlated with tanshinone and salvianolic acid synthesis. The present study provides a theoretical basis for further revealing the molecular mechanism of phosphorus regulation of growth, development, and secondary metabolism of S. miltiorrhiza and provides potential targets for efficient cultivation and molecular breeding of S. miltiorrhiza. Full article

Selenium (Se), as a vital trace element, plays an important role in regulating the antioxidant systems of plants, strengthening photosynthetic capacity, and enhancing their stress resistance. Selenate and selenite are the dominant forms of Se available to plants in soils. This research takes highland barley as the research object, aiming to assess the impacts of plant growth, organic acid metabolite, and six transcription factor families in highland barley seedlings under varying concentrations of Na₂SeO₃. The study indicated that compared to the control group (CK), the plant height of highland barley seedlings under Se1 (0.02 g/kg Na₂SeO₃) treatment significantly increased by 66%. Under the Se2 (0.2 g/kg Na₂SeO₃) treatment, plant height significantly decreased by 28%. With Na₂SeO₃ concentration increased, the pigment content, O₂⁻ production rate, and soluble protein content in highland barley seedlings decreased, while the contents of soluble sugar, MDA, and H₂O₂ increased. Se1 treatment was found to be more beneficial for the growth and development of seedlings. The organic selenium in leaves and roots under Se2 treatment significantly increased by 1105-fold and 188-fold, respectively. The most effective migration capability from soil to leaf under Se1 or Se2 treatment was up to 6.15 or 6.56, respectively. Based on metabolomics, 30 differential metabolites of organic acids were screened from highland barley seedlings under Na₂SeO₃ treatment and showed positive correlationships with organic selenium, inorganic selenium, and total selenium in highland barley seedling leaves. Through transcriptome analysis, heatmap analysis on six major categories of transcription factors (bHLH, MYB, NAC, WRKY, GATA, and HSF) was performed. Under Se2 treatment, approximately two-thirds of the transcription factors showed high expressions. We further screened 26 differentially expressed genes (DEGs) related to Na₂SeO₃ concentration. Based on correlation analysis, there were six genes in the bHLH family, five in MYB, three in NAC, five in WRKY, and three in the GATA and HSF families that showed positive correlations with 30 differential organic acid metabolites. These results enhance our understanding of the relationship between the organic acid metabolites and transcription factor expression in highland barley seedlings under Na₂SeO₃ treatment. Full article

Plant cuticular wax serves as a critical component for defense against biotic and abiotic stresses, with its biosynthetic pathway regulated by the ECERIFERUM (CER) gene family. This study presents the first genome-wide identification of 79 CER genes (CalCERs) in pepper (Capsicum annuum L.), which are distributed across all 12 chromosomes. Phylogenetic analysis classified CalCERs into five clades, with clade-specific conservation of exon–intron architectures and protein motifs. Promoter cis-element analysis revealed enrichment of light-responsive elements, abscisic acid (ABA), jasmonic acid (JA), and stress-responsive regulatory motifs, indicating multi-pathway regulation. Transcriptomic data highlighted tissue-specific expression patterns, such as the root-predominant express gene CalCER1-2 and the flower-specific express gene CalCER3-1. Under abiotic stresses (drought, salt, heat, and cold), CalCER4-2 and CalCER6-6 responded rapidly, while most genes showed delayed differential expression. Under biotic stress, CalCER3-1 and CalCER5-3 were upregulated, whereas CalCER2-2 exhibited pathogen-specific suppression, suggesting roles in modulating wax-mediated pathogen resistance. Hormone treatments revealed dynamic responses: CalCER2-2 was persistently ABA-inducible, while CalCER3-1 specifically responded to JA. This study underscores evolutionary conservation and species-specific expansion of the pepper CER family, linking their expression to wax biosynthesis and stress adaptation. These insights provide a foundation for enhancing stress resilience in crops. Future work should employ gene editing and metabolomics to validate functional mechanisms and optimize breeding strategies. Full article

The quality of rice is closely related to its planting mode. The rice produced in rice–crab co-cultivation fields often enjoy higher prices and consumption enthusiasm than traditional rice due to the use of fewer chemical inputs, making it a key target of commercial fraud. In this study, multi-element, stable isotope, metabolite analysis techniques were synergistically applied with chemometric methods to distinguish between crab-field rice and common rice. Seven elements (Se, Rb, Cu, Cd, Ag, V, and Zn), two stable isotopes (δ¹⁵N and δ¹³C), and nine metabolites were identified as the most important discriminant variables. The discriminant analysis model based on seven elements and two stable isotopes, or based on nine metabolites, can completely distinguish between crab-field rice and conventional rice. The isotope, elemental, and metabolic fingerprint spectra selected in this study provide effective support for the authenticity identification of crab-field rice. Full article

Natural polysaccharides (NPs), as a class of bioactive macromolecules with multitarget synergistic regulatory potential, exhibit significant advantages in diabetes intervention. This review systematically summarizes the core hypoglycemic mechanisms of NPs, covering structure–activity relationships, integration of the gut microbiota–metabolism–immunity axis, and regulation of key signaling pathways. Studies demonstrate that the molecular weight, branch complexity, and chemical modifications of NPs mediate their hypoglycemic activity by influencing bioavailability and target specificity. NPs improve glucose metabolism through multiple pathways: activating insulin signaling, improving insulin resistance (IR), enhancing glycogen synthesis, inhibiting gluconeogenesis, and regulating gut microbiota homeostasis. Additionally, NPs protect pancreatic β-cell function via the nuclear factor E2-related factor 2 (Nrf2)/Antioxidant Response Element (ARE) antioxidant pathway and Toll-like receptor 4 (TLR4)/nuclear factor-κB (NF-κB) anti-inflammatory pathway. Clinical application of NPs still requires overcoming challenges such as resolving complex structure–activity relationships and dynamically integrating cross-organ signaling. Future research should focus on integrating multi-omics technologies (e.g., metagenomics, metabolomics) and organoid models to decipher the cross-organ synergistic action networks of NPs, and promote their translation from basic research to clinical applications. Full article

To elucidate the regional flavor characteristics of sun-dried green tea (SDT) and their underlying influencing factors, a comprehensive analysis was conducted using metabolomics and flavoromics approaches. This study systematically examined SDT samples and their corresponding tea garden soils from 13 distinct regions in Yunnan Province. The results revealed that the SDT samples could be classified into two distinct groups based on their flavor profiles. Compared to the regions of Pa Sha (PS), Bang Dong (BD), Dong Ban Shan (DBS), Dong Guo (DG), Su Hu (SH), Gua Feng Zhai (GFZ), and Wu Liang Shan (WLS), the regions of Xin Nong (XN), Ba Ka Nuan (BKN), Mang Ang (MA), Man Nuan (MN), Bing Dao (BDao), and Bin Shan (BS) exhibited a significant upregulation of the tea polyphenols (TP)/free amino acids (FAA) ratio. The former group was characterized by a sweet mellow taste, while the latter displayed a stronger taste profile. Furthermore, the analysis of volatile compounds demonstrated that geraniol and linalool were significantly upregulated in the PS, BD, DBS, DG, BS, and BDao regions, which were associated with tender and floral aromas. In contrast, isophorone, 2-pentyl furan, 1-octanol, D-limonene, and benzaldehyde were markedly enriched in the XN, BKN, MA, MN, SH, GFZ, and WLS regions, contributing to sweet and honey-like aromatic profiles. Altitude and mineral element phosphorus are potential key factors affecting the regional flavor differences in SDT. Specifically, SDT cultivated at higher altitudes and in soils with elevated available phosphorus content exhibited a greater likelihood of accumulating sweet mellow and floral compounds. This study provides scientific evidence for understanding the characteristic flavor profiles of SDT across different regions, offering valuable insights into the factors contributing to regional flavor differentiation in tea production. Full article

Vegetative propagation of mulberry (Morus alba L.) via sapling methods, due to the ability to exponentially multiply lateral buds on stem cuttings to enhance rapid shoot formation, is crucial for sericulture industries. The sprouting of mulberry using stubbles is an emerging method for rapid and mass production of mulberry leaves, but the growth mechanisms associated with its use remain obscure. This study is the first to report how the differential stubble lengths from mulberry plants alter and modulate phytohormones and the associated mechanisms. This study seeks to evaluate the growth mechanisms by elucidating the phytohormone signature modulation in response to differential stubble lengths of 0 cm, 5 cm, 10 cm, 20 cm, and a control via targeted metabolomics analysis in mulberry leaves. The results consistently show that the use of differential stubble lengths of mulberry promoted growth, the number of buds, aboveground biomass, and branch and leaf weights by improving the net photosynthesis, transpiration rate, stomatal conductance, and intercellular CO₂ relative to the control. The differential stubble lengths not only caused contrasting responses in the contents of plant hormones, including salicylic acid (SA), abscisic acid (ABA), indole-3-acetic acid (IAA), jasmonic acid (JA), and gibberellin (GA), but also modulated higher elemental contents relative to the control. The results further reveal significant and positive correlations between the phytohormones and all growth, biomass, and photosynthetic parameters, highlighting the role of phytohormones in the sprouting and rejuvenation of mulberry stubbles. Meanwhile, the targeted metabolomics analysis identified a total of 11 differentially accumulated phytohormones in response to the differential stubble lengths, which were significantly implicated and enriched in three major pathways, including the biosynthesis of plant hormones (ko01070), metabolic pathways (ko01100), and the plant hormone signal transduction pathway (ko04575). The use of stubbles for rapid leaf production in mulberry plants is of great importance to improve early sprouting and cutting survival, as well as shortening growth and rooting time, and is highly recommended for the sericulture industries. Full article

Pinus yunnanensis Franch. is a common woodland species in the southwest of China. Its trunk frequently twists during growth, affecting timber quality. The explanation for the twisted-trunk formation is unknown. In this work, we examined the variety of endophytes and metabolites by comparing the straight and twisted trunk types of P. yunnanensis. The results showed that the twisted trunk had a distinct endosymbiont composition compared to the straight trunk. Pseudomonas and Craurococcus bacteria, as well as the fungus taxa Phaeosphaeria and Epichloë, spread significantly more in the twisted trunk compared to the straight trunk. However, there was less Dechloromonas in the twisted trunk. Metabolomic analysis revealed differences in metabolites in the straight and twisted trunks, which were associated with four metabolic pathways: beta-alanine metabolism, metabolism of Jasmonic acid and trans-Zeatin metabolism, linoleic acid metabolism, and pentose phosphate pathway. The compounds were linked to certain endophyte bacteria species. Our findings suggested that the twisted trunk was subjected to more stress than the straight trunk because of endosymbionts. Moreover, we speculated that hormone signal transduction and the absorption, transport, and utilization of phosphorus elements and their interaction with microorganisms may be closely connected to the formation of twists. This is the first study to characterize the microbiome and metabolome in the twisted trunks of P. yunnanensis, and the results enhance our understanding of the underlying causes of twisted-trunk formation in P. yunnanensis. Full article

Background: Scientific and rational fertilizer management can not only improve the yield and quality of hazelnut (Corylus heterophylla × Corylus avellana) but also reduce the negative impact on the environment. Methods: Liquid Chromatography–tandem Mass Spectrometry (LC-MS/MS) technology was used to reveal the contents of various metabolites in hazelnut seedlings, and differential metabolites were screened by principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). Results: The results showed that a total of 178 up-regulated differential metabolites (Fold change > 1) and 175 down-regulated differential metabolites (Fold change < 1) were detected in 6 comparison groups (DWF0 vs. DWF4, DWF0 vs. DWF5, DWF0 vs. DWF6, DWF4 vs. DWF5, DWF4 vs. DWF6, DWF5 vs. DWF6). Interestingly, the flavonoid metabolic pathway was dramatically enriched, and it was involved in each fertilization combination. The metabolites of the flavonoid pathway in different fertilized and unfertilized groups were compared and analyzed, which displayed that metabolites tricetin, eriodictyol, garbanzol, apigenin, and biochanin A were significantly up-regulated, while garbanzol and astraglin were significantly down-regulated. More interestingly, the determination of flavonoid content and real-time fluorescence quantitative polymerase chain reaction (qRT-PCR) displayed that the application of trace element water-soluble fertilizer could significantly enhance the flavonoid content and the expression of genes related to the flavonoid biosynthesis pathway, such as phenylalanine ammonia-lyase (PAL) and cinnamate 4-hydroxylase (C4H), with the DWF4 treatment displaying the most significant values. Conclusions: Overall, the application of trace element water-soluble fertilizer (especially the DWF4 treatment) markedly affected the changes in key metabolites of the flavonoid pathway and the expression levels of key genes, thus promoting the growth and development of the hazelnut, which offers an important starting point for future analysis through genetic engineering. Full article

Under conditions of increasing anthropogenic load, aquatic ecosystems all over the world are undergoing a transformation, expressed in the growth of eutrophication, the overgrowing of water bodies with higher vegetation of macrophytes, cyanobacterial bloom, and the increased concentrations of different pollutants in these objects. In the region of Eastern Siberia that we studied, located in the middle reaches of the Lena River basin, there is the city of Yakutsk—the largest city in the world built in a permafrost region. Within the city and its surroundings, there are many small lakes (less than 1 km² in area) which over the past decades have been subject to varying degrees of pressure associated with human activity (nutrients and organic matter loads, urban landscape transformation). This study is the first to combine the metabolomic profiling of Potamogeton perfoliatus with microalgal bioindication to assess anthropogenic impacts in permafrost urban lakes, providing a novel framework for monitoring ecological resilience in extreme environments. We studied four lakes with varying degrees of anthropogenic pressure. Using a comprehensive assessment of the bioindicator properties of planktonic microalgae and the chemical parameters of water using statistical methods and principal component analysis (PCA), the lakes most susceptible to anthropogenic pressure were identified. Concentrations of pollutant elements in the tissues of the submerged macrophyte aquatic plant Potamogeton perfoliatus L., which inhabits all the lakes we studied, were estimated. Data on the content of pollutant elements in aquatic vegetation and the results of metabolomic analysis made it possible to identify the main sources of anthropogenic impact in the urbanized permafrost area. The pollution of water bodies with some key pollutants leads to Potamogeton perfoliatus’s metabolites decreasing, such as sucrose, monosaccharides (arabinose, mannose, fructose, glucose, galactose), organic acids (glyceric acid, malic acid, erythronic acid, fumaric acid, succinic acid, citric acid), fatty acids (linoleic and linolenic acids), myo-inositol, 4-coumaric acid, caffeic acid, rosmarinic acid, shikimic acid, and catechollactate, caused by pollution which may decrease the photosynthetic activity and worsen the sustainability of water ecosystems. Linkage was established between the accumulation of pollutants in plant tissues, the trophic status of the lake, and the percentage of eutrophic microalgae, which can be used in monitoring the anthropogenic load in the permafrost zone. Knowledge of the composition and concentration of secondary metabolites produced by macrophytes in permafrost lakes can be useful in organizing water resource management in terms of reducing the level of cyanobacterial blooms due to allelochemical compounds secreted by macrophytes. This new work makes possible the evaluation of the permafrost-zone small-lake anthropogenic load in the frame of a changing climate and the growing attention of the industry to Arctic resources. Full article

Zucchini (Cucurbita pepo subsp. pepo) is a seasonal vegetable (also known as courgette) characterized by health properties due to the content of several bioactive molecules. For this reason, the consumption of zucchini is highly recommended as a part of the Mediterranean diet. The aim of this study was to evaluate the possible influence of a specific compost supply for shifting the characteristics of an integrated agriculture toward a biodynamic standard following Demeter^® certified rules. In particular, an approach based on ¹H-Nuclear Magnetic Resonance (NMR) spectroscopy and multivariate statistical analysis (MVA) was applied to analyze the differences between the metabolic profiles of the zucchini samples (with the same cultivar, Vitulia), obtained from three different agronomical practices: two focused agricultural systems (compost supplied and integrated), as well as the used benchmark (Demeter biodynamic certified). The obtained results showed that the samples from the plots managed with biofertilizer from compost showed similar behaviour to the samples managed under Demeter biodynamic certification, with higher content of some amino acids, such as arginine, and lower content of sugars than the samples from integrated farming. The concentration of twenty elements was then determined using inductively coupled plasma atomic emission spectroscopy (ICP-AES). The averaged results of the elemental data appear almost parallel to the trend observed with the metabolomics approach. In the present case, the use of a specific compost as a biofertilizer has shown to promote the transition to the quality standards of the Demeter certification, significantly improving the crops’ sustainability. Full article

The advancement of multi-omics tools has revolutionized the study of complex biological systems, providing comprehensive insights into the molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify and characterize biological elements that contribute to phenotypic traits. This review delves into recent progress in applying multi-omics approaches to elucidate the genetic, epigenetic, and metabolic networks associated with key traits in plants. We emphasize the potential of these integrative strategies to enhance crop improvement, optimize agricultural practices, and promote sustainable environmental management. Furthermore, we explore future prospects in the field, underscoring the importance of cutting-edge technological advancements and the need for interdisciplinary collaboration to address ongoing challenges. By bridging various omics platforms, this review aims to provide a holistic framework for advancing research in plant biology and agriculture. Full article