Background: When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available. Results: To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism. Conclusion: Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance.

Introduction: Drought stress is a major abiotic factor limiting sugarcane productivity. However, the molecular mechanisms conferring drought resistance in sugarcane are not fully elucidated, which hinders the breeding of resilient varieties. Methods: Three experimental sugarcane varieties were subjected to polyethylene glycol (PEG6000)-simulated drought stress. Subsequent transcriptomic analysis was performed by integrating second-generation (Illumina) and third-generation (PacBio) sequencing technologies. This approach yielded a comprehensive transcriptome landscape. Bioinformatics analyses included gene annotation, differential expression screening, Weighted Gene Co-expression Network Analysis (WGCNA), and network visualization using Cytoscape. Results: Sequencing generated a total transcript length of 77,930,985 bp, identifying 40,359 unique genes, with 38,791 successfully annotated. Under drought stress, the variety ZZ9 exhibited significant enrichment and upregulation of metabolic pathways related to photosynthesis, plant hormones, polysaccharide synthesis, and amino acid metabolism. Several transcription factor families, including bHLH, bZIP, ERF, NAC, MYB, and GRAS, were drought-inducible. WGCNA identified 22 co-expression modules, with the MEten module showing the highest correlation with drought response. Key hub genes within MEten included NACA1, ABA-related genes, ERA1, PER70, ATX, two superoxide dismutase genes (SODF1 and SODF2), two late embryogenesis abundant (LEA) genes, and two lipoxygenase (LOX) genes. Furthermore, Cytoscape-based analysis pinpointed the novel gene PSY1 and two additional candidates potentially involved in photosynthetic regulation during drought. Discussion: By integrating multi-platform transcriptomics and systems biology approaches, this study delineates potential molecular regulatory networks underlying drought resistance in sugarcane. The identified hub genes and pathways provide critical resources for future functional genomics studies and molecular breeding programs aimed at enhancing drought tolerance in sugarcane.

Panax notoginseng is a valuable medicinal herb, but its sustainable production is constrained by long cultivation cycles and continuous cropping obstacles. Adventitious root culture presents a viable alternative. This study establishes a robust and sustainable platform for the efficient production of ginsenosides in P. notoginseng adventitious root cultures. We first systematically optimized the culture system, identifying leaf segments as the optimal explant due to their high callus induction rate (95.77%), low contamination, and renewable nature. Combined with optimized bioprocess parameters (3 g/L inoculation density, 50 g/L sucrose), this strategy addressed key practical bottlenecks. Beyond methodological advancement, our research provides novel mechanistic insights into the action of methyl jasmonate (MeJA). A key finding is the discovery that MeJA functions as a ‘precision metabolic switch,’ differentially regulating a critical branch point in the saponin pathway. It coordinately upregulates the protopanaxadiol (PPD)-type gene CYP716A47 while downregulating the protopanaxatriol (PPT)-type gene CYP716A53v2 that genetically explains the directed enrichment of specific ginsenosides. This integrated approach not only advances the fundamental understanding of elicitor action but also provides a scalable and controllable system for the industrial production of P. notoginseng phytopharmaceuticals with tailored saponin profiles.

Introduction: Sugarcane is primarily propagated for large-scale agricultural production through vegetative reproduction by planting stem cuttings. Development of sprout and sett root from the cuttings is essential for sugarcane plant to adapt to the field environment. We observed asynchronous development during the sprouting of stem cuttings in two sibling sugarcane cultivars sharing the same parent in cross breeding: the axillary buds of cultivar ZZ2 (ZZ2B) sprout earlier, while the sett roots of ZZ9 (ZZ9R) emerge sooner.Methods: Comparison of the sett root architecture, soluble sugar content, plant hormone levels and gene expression profiles during sprouting.Results: We found that ZZ9 has a lower root cortex thickness ratio and a higher vascular cylinder thickness ratio. We also identified significant differences in the levels of soluble sugars, 3-Indolebutyric acid (IBA), N6-isopentenyladenosine (IPA), cis-Zeatin (cZ), Abscisic Acid (ABA), Gibberellin A3 (GA₃), Gibberellin A7 (GA₇), (±)-Jasmonic acid (JA), and N-((-)-jasmonoyl)-Sisoleucine (JA-Ile) between these cultivars. cuttings. In addition, we identified differentially expressed genes through transcriptomic analysis and discovered, via GO and KEGG enrichment analyses, that negative regulation of external stimulus response is a key to the preference of ZZ2 for early bud sprouting. The Twin-arginine translocation complex (Tat) significantly influences the preference of ZZ9’s root emergence. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that specific metabolic processes in seed coat mucilage uniquely determine the asynchronous development of sett roots and axillary buds.Discussion: These findings provide a theoretical foundation and new perspective for understand asynchronous development in sugarcane production, offering novel insights for breeding high-quality varieties.

Background: When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available.Results: To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism.Conclusion: Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance.