The flowers of Panax ginseng C. A. Mey. (PG) and Panax notoginseng (Burkill) F. H. Chen ex C. H. Chow (PN) are morphologically indistinguishable after drying, leading to prevalent adulteration that compromises product quality and consumer safety. To address this issue, we developed a rapid, closed-tube molecular authentication method based on high-resolution melting (HRM) analysis. Species-specific primer pairs were designed to target the conserved ITS and rbcL-accD regions, with PNG-2 selected as the optimal candidate owing to its stable genotyping performance and moderate GC content. Our results established GC content, rather than amplicon length, as the primary determinant of the melting temperature (Tm). Notably, the experimentally measured Tm values were consistently 0.7–1.5 °C higher than theoretical predictions, a discrepancy attributable to the stabilizing effect of the saturated fluorescent dye. To ensure maximum diagnostic reliability, the HRM results were cross-validated through a three-tier system comprising ITS2 phylogenetic analysis, agarose gel electrophoresis, and Sanger sequencing. The practical utility and matrix robustness of the assay were further verified using a diversified validation cohort of 30 commercial samples, including 24 floral batches and 6 root-derived products (root slices and ultramicro powders). The HRM profiles demonstrated 100% concordance with DNA barcoding results, effectively identifying mislabeled products across different botanical matrices and processing forms. This methodology, which can be completed within 3 h, provides a significantly more cost-effective and rapid alternative to traditional sequencing-based methods for large-scale market surveillance and industrial quality control.

Considering the prevalence of cropping pattern in many Saffron cultivation regions, the continuous cropping obstacle caused the decline in growth and development. These effects justify the necessity of studying agronomic strategies to promote plant quality and production. Herein, the mono cropping, intercrop of Paulownia and Saffron, and intercrop of Soybean and Saffron patterns have been performed. The metabolites of Saffron under three cropping patterns were determined and identified using by an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. Uni and multivariate statistical analysis were applied to examine the difference between groups and select the significant differential accumulated metabolites. The results showed that a total of 315 compounds were significantly changed in three comparison groups. Phenylalanine metabolism, linoleic acid metabolism, and flavonoid biosynthesis pathway has been greatly enriched by the changed metabolites. The phenyl lactate, trans-2-Hydroxy-cinnamate, γ-Linolenate, 9-oxo-octadecadienoic acid, 13-0xo-0ctadecadienoic acid, 9,12,13-TriHOME of those metabolites showed significant differential accumulation in Saffron under three cropping patterns. And the accumulation of safranal and picrocrocin related compounds, such as Crocetin, Crocin showed a similar variation regularity. These indicate that there may be a close internal relationship between the cropping pattern and the biosynthesis of metabolites related to endogenous substances and Saffron quality formation.

Isatis indigotica Fort.—a well-known medicinal cruciferous species—is the source plant of Isatidis Radix and Folium Isatidis, and is widely cultivated for medicinal raw material. The silique serves as the propagative organ for seed production of I. indigotica, and its developmental performance directly determines the plant’s seed quality and seed multiplication efficiency. To decipher the physiological and molecular mechanisms by which exogenous salicylic acid (SA) and indole-3-acetic acid (IAA) modulate silique development, we performed a field experiment using the cultivar ‘Songming No. 1’. Plants were foliar-sprayed with 2 mmol·L⁻¹ SA at the full-bloom stage and 0.571 mmol·L⁻¹ IAA at the flower-bud stage, with distilled water treatment serving as the control (CK). Silique samples were collected at five key developmental stages: formation, growth, expansion, browning maturation, and full maturation. We measured nutrient contents, carbohydrate-metabolizing enzyme activities, and endogenous phytohormone levels, and performed integrated transcriptomic and untargeted metabolomic analyses. Exogenous SA and IAA substantially reshaped the accumulation patterns of sucrose, starch, soluble proteins, and other nutrients. The activities of invertase, pyruvate kinase (PK), glucose-6-phosphate dehydrogenase (G6PDH), and soluble starch synthase (SSS) were significantly altered by hormone treatments; SA accelerated metabolic processes in early-stage siliques. Transcriptomic screening identified nine SA-responsive genes and one IAA-responsive candidate gene. SA mainly perturbed carbohydrate and amino acid metabolic pathways, whereas IAA modulated terpenoid and polyketide biosynthetic pathways. A total of 7028 metabolites were annotated, showing that SA exerted stronger effects on carbohydrate metabolism than IAA. Nine-quadrant correlation analysis identified multiple gene–metabolite modules associated with silique development. Collectively, this study characterizes the physiological and multi-omics responses of I. indigotica siliques to exogenous SA and IAA. The physiological and molecular alterations observed here are consistent with the phenotypic outcomes reported under identical experimental treatments. This work provides valuable resources for exploring hormone-mediated high-quality seed propagation and candidate gene mining in I. indigotica.

Different from the normal circular-stem plants, the Chimonobambusa utilis presents an unusual square-like culm. Bamboo culms can alter its shape by adjusting the expression patterns of genes for appealing different living conditions. However, underling mechanism for biomolecular function and regulation patterns of square-like culm is still absurd. Multi-omics analysis can be applied for revealing its molecular biological mechanism. In our study, phenotypic analysis suggested that change of stem wall thickness (STW) showed a trend of corner region (CR) > side region (SR), and fibre wall thickness (WT) showed a trend of SR > CR. It has been showed that there is an intrinsic correlation between Lignin content and cell wall thickness. Based on the anatomical features, FTIR spectroscopy analysis suggested that the relative lignin content at SR was higher than CR. It suggested that the deposition of lignin at CR and SR was different with each other. Therefore, the phenotypic analysis combined with transcriptome and metabolome were performed for identifying differential expressed genes and the relative metabolic pathways. Transcriptome results suggested that lignin biosynthesis related genes were up-regulated at SR. Metabolome results suggested that lignin precursors at SR accumulated more that CR and significantly enriched in phenylpropanoid biosynthesis KEGG pathway. These findings indicate that lignin accumulation that has a great possibility for change, leading to change of lignin content at different circumferential positions accordingly. It is suggested a coherence in phenotypic, chemical components, transcriptome, metabolome analysis. It is concluded that lignin biosynthesis related genes were up-regulated at SR which caused lignin biosynthesis precursors accumulated more at SR, leading to lignin content at SR was higher than at CR. After that, in position of the SR, cells have been enlarged. For those, the stem changed from its morphology from circle to square. The findings manifest the regulation mechanism of lignin related genes on the square-like stem. The analysis method provides an innovative means for revealing the molecular biological mechanism involved in the formation of non-circular plant.