Phosphorus is an essential element for plant growth, and its deficiency severely limits crop productivity. To explore genetic resources for improving phosphorus use efficiency, this study investigated the differential low-phosphorus tolerance mechanisms of two kudzu (Pueraria lobata) germplasms from Australia (tolerant) and Jiangsu, China (sensitive) using hydroponics, RNA-seq, and WGCNA. The results showed that the Australian germplasm exhibited superior low-phosphorus tolerance through root morphological plasticity, which was characterized by increased root length and tip number under low phosphorus (0.05 mmol L-1 KH2PO4); enhanced reactive oxygen species scavenging, with higher peroxidase and catalase activities under extremely low phosphorus (0.005 mmol L-1 KH2PO4), and extensive transcriptome reprogramming, including 8896 upregulated genes in response to phosphorus deficiency. In contrast, the Jiangsu germplasm showed limited adaptive responses, with reduced root hairs and biomass under stress. WGCNA partitioned 21,734 expressed genes into 20 co-expression modules, among which the turquoise and light green modules showed significant correlations with phosphorus treatments and phenotypic traits. Genes in the turquoise module were primarily enriched in oxidative phosphorylation and phenylpropanoid biosynthesis pathways, whereas the light green module was significantly enriched in ribosome-related pathways. Five hub genes, ABCG5, TALDO, VAMP7B, EEF1AS, and RPLP0, were identified as core components of these modules. Collectively, these findings establish the Australian kudzu as a valuable germplasm resource for improving phosphorus use efficiency in crops and provide key molecular targets for precision breeding.

Tree stem cells are primarily localized in the apical meristems, including the shoot apical meristem (SAM) and the root apical meristem (RAM), as well as in the lateral meristems, specifically the vascular cambium. Through continuous division and differentiation, these stem cells drive both vertical and radial growth in trees. This review systematically examines recent research progress on tree stem cells, with a focus on their structural organization and characteristics, mechanisms of maintenance and regulation, and potential applications. Structurally, tree stem cells exhibit pronounced tissue specificity and clear functional differentiations. With respect to regulatory mechanisms, their maintenance and differentiation are coordinately controlled by genetic networks such as CLV-WUS, WOX and HD-ZIP III/KANADI, environmental factors such as drought, salinity and extreme temperatures, and plant hormones, including auxins, cytokinins, abscisic acid and gibberellins. In terms of applications, research on tree stem cells provides key technological support for invitro cell culture, large-scale production of bioactive compounds from forest products, and sustainable wood utilization. This paper summarizes recent domestic and international research on tree stem cells, highlighting their regulatory mechanisms, physiological characteristics, and application prospects. Furthermore, it discusses current challenges and future directions in this field, with the aim of informing efforts in forest genetic improvement and the sustainable development of tree resources.

Houttuynia cordata is a traditional medicinal plant with various bioactivities mainly caused by its terpenoids. However, the effects of geography, environment, biosynthesis, and multiple pharmacological targets of these compounds are still not well understood. We used UPLC-MS/MS and GC-MS metabolomics to analyze terpenoids in accession 7# grown across six regions in China (Yunnan, Guangxi, Hubei, Chongqing, Guizhou, and Sichuan) and identified key environmental factors linked through random forest analysis. Network pharmacology identified potential targets and pathways for differentially accumulated terpenoids, further validated by molecular docking. Transcriptome sequencing identified terpenoid biosynthetic genes. A total of 502 terpenoid metabolites were detected, and chemotypic diversity was strongly shaped by geographical origin. Altitude (bio21) and annual precipitation (bio12) emerged as the primary environmental factors associated with 58 and 18 differential metabolites, respectively. Network analysis of 39 terpenoids revealed 239 potential targets, with 23 core targets (e.g., ESR1, STAT3, BCL2, AR) enriched in cancer, endocrine resistance, and hormone-related pathways. Docking confirmed stable interactions between key terpenoids (byzantionoside B, ursonic Acid) and core targets (ESR1, AR, BCL2) with binding energies < -7.5 kcal mol-1. Transcriptomic analysis uncovered 103 differentially expressed genes in the MVA and MEP pathways, with several (e.g., AACT, FPPS, HMGR, DXS) showing strong correlations with core terpenoid accumulation. This multi-omics study provides insights into substantial geospatial variation in H. cordata terpenoids, identifies altitude and precipitation as major environmental factors associated with terpenoid accumulation, and offers a predictive framework for the biosynthetic network and multi-target pharmacological potential, especially anticancer. It offers a theoretical basis for quality control and optimized cultivation.

This study presents an integrated multivariate and univariate analysis of circadian metabolomic signatures in Ilex paraguariensis (yerba mate) clones cultivated under semi-hydroponic conditions. Using repeated measures ANOVA-Simultaneous Component Analysis (RM-ASCA+) and hierarchical clustering on principal components (HCPC), we explored clone-specific and photoperiod-dependent metabolic responses across light and dark phases, complemented by high-resolution timepoint sampling (HRS) and targeted screening. Clone EC21 exhibited elevated levels of sugars, amino acids, and organic acids, suggesting a metabolic strategy adapted to saline stress and nocturnal energy demands. Photoperiod effects revealed circadian regulation of central carbon metabolites (e.g., glucose, fructose, maltose) and phenylpropanoid intermediates linked to bioactive compounds such as caffeoyl-quinic acids. Interaction effects highlighted metabolic plasticity, particularly in nitrogen assimilation, with compounds like 2-oxo-glutaric acid, glutamine, and ornithine showing clone-specific temporal patterns. Caffeine, a heritable and physiologically relevant metabolite, displayed distinct circadian profiles. EC24 accumulated caffeine during the day, while EC21 peaked at night. This dynamic distribution, supported by allantoin patterns in caffeine catabolism, suggests divergent nitrogen turnover strategies between clones. These findings underscore the importance of genotype selection and temporal regulation in optimizing yerba mate performance under semi-hydroponic systems. The combined use of RM-ASCA+ and univariate analysis proved to be a powerful approach for profiling metabolomic rhythms, offering valuable insights for breeding programs targeting bioactive compound enhancement, stress resilience, and metabolic efficiency.

Nitrogen fertilization remains a cornerstone of modern agriculture, yet its excessive use contributes to environmental degradation. Rapeseed (Brassica napus L.) is notably inefficient in N uptake, highlighting the importance of root traits that enhance soil exploration and nutrient acquisition. This study investigated root transcriptomic responses to nitrate availability across rapeseed genetic diversity. A panel of 40 lines was screened on vertical agar plates, revealing substantial variation in root morphology, strong heritability, and genetic control. Low nitrate supply increased the root-to-shoot biomass ratio and stimulated lateral root proliferation. Transcriptomic profiling was then conducted on three genotype pairs selected to represent distinct root system sizes. Hydroponically grown plants were exposed to two divergent nitrate levels for 24 h, and root tissues were harvested for RNA sequencing. Differential expression analysis identified over a 1000 genes significantly induced or repressed by nitrate treatment, with only 10% shared across genotypes. Gene ontology enrichment analysis revealed a central nitrate-responsive transcriptional program, accompanied by distinct molecular signatures associated with root size. Co-expression network analysis identified regulatory modules that integrate nitrate transporters with auxin signaling and energy metabolism. These modules also uncovered roles for glucosinolate biosynthesis and aquaporin-mediated water transport. This study provides a set of candidate genes and regulatory networks that represent promising targets for breeding rapeseed varieties with optimized root traits for sustainable agriculture.

As a medicinal and culinary important species, Codonopsis pilosula requires comprehensive germplasm research and innovation. This study elucidated the molecular mechanisms underlying stem pigmentation in C. pilosula through integrated transcriptomic and metabolomic analyses. Comparative profiling of purple-stemmed (CZ) and green-stemmed (CL) cultivars revealed 8674 differentially expressed genes (DEGs) and 105 differentially expressed metabolites (DEMs). Notably, the CZ cultivar demonstrated elevated levels of procyanidin B2, delphinidin, and four cyanidin derivatives, exhibiting 44.6-fold higher total anthocyanin content compared to the CL cultivar. This phenotype was associated with the coordinated regulation of MYB/bHLH transcription factors and structural genes (including F3'5'H, ANS, and CHS). Multi-omics networks identified flavonoid biosynthesis (enriched with 30 DEMs) and redox regulation (involving 23 antioxidant-related DEGs) as pivotal pathways. Enhanced catalase (CAT) and peroxidase (POD) enzymatic activities, coupled with increased accumulation of proline and raffinose, together with anthocyanin-mediated reactive oxygen species (ROS) scavenging, were associated with enhanced stress tolerance in the CZ cultivar. Key transporters (such as GSTU45 and MATE30), potentially involved in vacuolar anthocyanin deposition, were characterized. These findings provide novel insights into metabolic regulation and molecular breeding strategies for medicinal plant quality improvement, primarily through understanding the mechanisms underlying stem-specific anthocyanin accumulation and associated stress resilience.

Salinity stress severely limits crop production, particularly in arid and semi-arid regions. This study explored the potential of zinc oxide nanoparticles (ZnO-NPs) as a priming agent to enhance castor (Ricinus communis) seedling growth under salt stress (100 mM NaCl), focusing on metabolic reprogramming and storage reserve mobilization. ZnO-NPs priming significantly improved seedling vigor by enhancing lipid mobilization, reducing triacylglycerol (TAG) accumulation, and promoting fatty acid breakdown, especially in the cotyledons. This was accompanied by upregulation of key enzymes in the glyoxylate and tricarboxylic acid (TCA) cycles, facilitating the conversion of stored lipids into soluble sugars for energy. Furthermore, priming restored ATP levels, particularly in the radicle, thereby improving energy metabolism. ZnO-NPs also mitigated oxidative stress, reducing lipid peroxidation and preserving membrane integrity. Transcriptomic analysis revealed upregulation of genes involved in lipid metabolism, stress responses, and energy conversion, supporting the biochemical changes observed. These findings highlight ZnO-NPs as a promising strategy to enhance seedling establishment and crop resilience under salt stress, contributing to sustainable agricultural practices and improved salt tolerance in oilseed crops.

Fruit ripening, the penultimate stage before senescence, is exclusively regulated by light, which signals and activates ripening-specific genes. Building on light's regulatory role in development, this review updates on signaling pathways, including phytochrome, cryptochrome, phototropins, and wavelength receptors, that are involved in gene activation during ripening. Understanding CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5) as the principal hub of light perception and downstream modulation for transcriptome, proteome, and metabolome activities, the synergism of hormonal influence is discussed. The precise wavelengths of light and their effects on major growth hormones, such as ethylene, abscisic acid (ABA), and auxin, are discussed in relation to the progression of ripening metabolism and the regulation of specific transcription factors. This review points out regulatory factors like ETHYLENE RESPONSE FACTOR E4 to alter auxin's promoter binding activity, allowing ethylene sensitivity. The major focus is on ethylene response factors, MADS-box genes, and bZIP proteins for the molecular regulation of ripening-induced fruit coat hydrolysis, aroma production, and respiratory burst. The genetic mutation was elucidated in the context of the RIPENING INHIBITOR (RIN) and NON-RIPENING (NOR) factors in tomato genotypes, which share similar sequences with other crops, such as strawberry. The review also highlights epigenetic control through chromatin remodeling, methylation/demethylation reactions, and histone modifications, providing further insight into the light's influence on the extra-transcriptome affair. Collectively, this review concludes that light is a major molecular switch in pathways of hormonal, genetic, and epigenetic functions, contributing to advances in postharvest preservation.

Increasing soil salinization in the Songnen Plain region, Northeast China, has hindered common bean (Phaseolus vulgaris L.) cultivation. The specific regulatory mechanisms of sugar metabolism in common bean leaves under alkaline salt stress remain unclear. To address this research gap, in China's Songnen Plain, we subjected the high-yielding and multi-resistant granular bean variety "Qingyun 1" seedlings to stress treatments at 0, 24, and 48 h time points. Alkaline salt stress was simulated by applying 100 mM NaHCO3 and Na2CO3 mixed at a 9:1 M ratio. With prolonged treatment time, common bean leaves gradually wilted and yellowed. Stomatal conductance, total chlorophyll, and carotenoids significantly decreased by 16.45%-75.77%. Superoxide dismutase, peroxidase, and catalase activities and malondialdehyde and H2O2 contents significantly increased by 42.04%-91.36%, all reaching extremely significant levels (p < 0.01). Under progressive photosynthesis inhibition, the dynamic regulatory network of sugar metabolism helped sustain common bean leaf responses to alkaline salt stress. Integration of the dynamic changes in the activities of hexokinase (HK), α-galactosidase (galA), and 6-phosphofructokinase with the levels of sugars resulted in persistently suppressed HK phosphorylation, enhancing galA activity accelerated stachyose and raffinose metabolism and Suc and Fru release promotion in the leaves under alkaline salt stress. This ensured sustained high SS concentrations, ultimately providing plants with additional energy and carbon sources. Thus, the key genes encoding galA could be important candidates for exploring alkaline salt stress response mechanisms in common bean. These findings provide insights and theoretical support for breeding new alkaline salt-tolerant common bean varieties.

Carbon dynamics are essential for understanding plant drought adaptation, yet how desert shrubs coordinate photosynthesis, growth, and storage under drought remains unclear. We quantified light-saturated photosynthetic assimilation rate (Asat), leaf absolute growth rate (AGR), and whole-plant non-structural carbohydrates (NSCs) in two dominant desert shrubs, Haloxylon ammodendron and H. persicum, across a water-stress gradient associated with groundwater depth, precipitation exclusion, and seasonal drying, using predawn leaf water potential (ΨPD) as an integrative index of plant water status. Furthermore, we evaluated linkages among ΨPD, Asat, AGR, and NSCs. AGR declined faster than Asat as ΨPD decreased, suggesting the photosynthesis-growth decoupling at the leaf level under increasing water stress. While whole-plant NSCs remained stable, organ-specific starch and soluble sugar patterns diverged between species: H. ammodendron accumulated starch in branches, whereas H. persicum increased leaf starch concentrations and decreased sugar:NSCs ratios, with opposite trends observed in the roots. Moreover, Asat was negatively correlated with branch starch concentrations in H. ammodendron, but negatively correlated with leaf starch concentrations in H. persicum. The relationships between AGR and branch starch concentrations tended to be negative in H. ammodendron, whereas leaf and root NSCs were negatively related to AGR in H. persicum. These findings suggest that aboveground organs adopt conservative carbon utilization strategies under drought, while belowground organs shift toward acquisitive strategies, highlighting contrasting carbon use patterns that may enhance drought survival in desert shrubs.