To investigate how Yunnan's distinctive geographical and climatic conditions shape the unique metabolic profile of its cigar tobacco leaves (CTLs), and to establish a reliable method for origin traceability using machine learning, a non-targeted metabolomics analysis was conducted on 71 CTL samples collected from the Dominican Republic, Indonesia, and Yunnan, including Lincang, Pu’er, and Yuxi within Yunnan. A total of 778 highly reliable metabolites were identified. Influenced by Yunnan's high altitude, large diurnal temperature variation, intense ultraviolet radiation, and relative dryness, its CTLs exhibited characteristic metabolic profiles, with significant enrichment in pathways such as flavone and flavonol biosynthesis and betalain biosynthesis. Elevated levels of polyphenols, indoles, jasmonates, carotenoids, and other compounds were linked to Yunnan CTLs' distinct woody, roasted, and astringent flavor profile. Twelve key biomarkers were selected using Multivariate methods with unbiased variable selection in R (MUVR). Machine learning algorithms—including LDA, LR, GMM, KNN, and SVM—were applied to these biomarkers, achieving highly accurate origin discrimination across national (Yunnan vs. Dominican Republic/Indonesia) and regional (Lincang, Pu’er, Yuxi) scales. Validation results showed a median false classification rate of 0.1 over 100 iterations and an AUC close to 1, confirming the model's high accuracy and robustness for CTLs origin traceability.

Stacking, a pivotal step in the preparation of composted organic manures, plays a crucial role in organic matter decomposition, nutrient availability, and soil microbial diversity, with effects dependent on the stacking duration. However, the mechanisms through which organic manures with different stacking times influence crop growth and development via alterations in the soil environment remain poorly understood. This study employed a pot experiment with tobacco plants, applying conventional fertilizers alongside organic cottonseed meal manures subjected to various stacking times (0, 10, 20, and 30 days). The primary aim was to examine the impact of cottonseed meal organic manures on the microbial community structure, function, and chemical properties of tobacco-growing soil, as well as to assess dry matter accumulation in tobacco plants. Results revealed that, compared to conventional fertilizers alone, the addition of cottonseed meal organic manures significantly enhanced soil organic matter content, with the 20d-stacked manure showing the highest increase (68.94%). Additionally, the composition of the soil microbial community was modified, which has increased the relative abundance of carbon and nitrogen metabolic functions. Dry matter accumulation in tobacco plants increased by 13.66%, 25.83%, 31.65%, and 9.69% across the different stacking times. In conclusion, composted organic manures regulate the soil-microbe system, promoting tobacco growth by enhancing the microbial structure of rhizosphere soil and improving nutrient availability. Cottonseed meal organic manures subjected to 20d of composting exhibited the most comprehensive benefits. The enrichment of beneficial microbes like Chryseobacterium and Humicola (potential antagonists of soil pathogens) might contribute to the observed enhancement in soil organic matter and available nutrients. This improvement in soil quality led to a balanced nutrient environment, ultimately promoting dry matter accumulation in tobacco plants. These findings offer robust theoretical support for the application of composted organic manures.IMPORTANCEThis study is important because it elucidates the crucial mechanisms by which composted organic manures, specifically through the regulation of the soil-microbe system, promote crop growth. It provides key evidence that the stacking duration is a critical factor, identifying a 20-day (d) composting period for cottonseed meal manure as optimal for delivering comprehensive benefits: (i) Enhanced soil health: significantly increasing soil organic matter and improving nutrient availability. (ii) Improved microbial community: shifting the soil microbial structure to favor beneficial bacteria and suppress pathogens, thereby enhancing metabolic functions related to carbon and nitrogen cycling. (iii) Direct crop promotion: leading to a substantial increase in dry matter accumulation in tobacco plants.

Chromium (Cr) contamination severely inhibits plant productivity, primarily by disrupting photosynthetic performance, growth, and inducing oxidative stress. This study investigated the comparative molecular mechanisms by which exogenous glutathione (GSH) and melatonin (MT) confer tolerance to Cr stress in sweet potato using an integrated transcriptomic approach. Transcriptome analysis identified 7,734 differentially expressed genes (DEGs) across Cr stress and mitigator treatments. The GO and KEGG pathway enrichment analyses showed that DEGs were mainly enriched in GO terms, such as photosynthesis, carbon fixation, and cell-wall organization, as well as pathways including MAPK signaling, glutathione metabolism, plant hormone signal transduction, and membrane/vesicle transport. These DEGs were subjected to cluster analysis, and four major expression clusters (C1-C4) were identified, with DEGs ranging from 1,234 to 3,285. GSH-specific protection was associated with Cluster C4, enhancing genes involved in ROS defense, H2O2 response, pyruvate metabolism, and ER protein processing, indicating improved redox and metabolic control Network analysis identified 30 potential key hub genes, including the growth regulator GA20OX1, the chlorophyll synthesis enzyme HEMA1, and the vacuolar transport aquaporin TIP2-1. These results suggest that GSH induces a stronger transcriptional response by effectively mitigating Cr-induced damage and strengthening a redox-centered defensive metabolic network. This identifies actionable molecular targets for crop improvement through breeding and genetic engineering.

Soil salinity is a major constraint on crop productivity, and plants rely on multilayered regulatory mechanisms to adapt to stress. Alternative splicing (AS) enhances transcriptome plasticity, yet how light modulates AS under salt stress remains unclear. Here, we performed a transcriptome-wide analysis to investigate light-dependent AS dynamics in sweet potato under salt stress. Plant treatments were initiated during daytime (SD) and nighttime (SN) conditions, and samples were collected at five time points (0-8 h). Intron retention (IR) was the predominant AS type (~36-37%), followed by A3SS, A5SS, and exon skipping (SE). Notably, light enhanced both the magnitude and temporal dynamic of AS, with a pronounced early response (0-2 h) under SD, where differential AS (DAS) events were nearly doubled compared with SN. This early AS response was accompanied by an increased prevalence of IR events and upregulation of spliceosome-related genes, suggesting dynamic splicing regulation under light. Enrichment of the mRNA surveillance pathway further indicates that IR-derived transcripts may be subject to RNA quality control. Although enriched pathways were largely conserved between SD and SN, including spliceosome and mRNA surveillance, more DAS genes under SD indicate enhanced responsiveness of conserved regulatory networks. These findings demonstrate that light reshapes the temporal dynamics of AS under salt stress, primarily through IR and its coupling with RNA surveillance, providing new insights into post-transcriptional regulation in crop stress adaptation.

High summer temperatures increasingly constrain sweet cherry production, yet field-validated assessments of rootstock resilience remain scarce. To fill this gap, this study presents a pioneering multidimensional evaluation of five widely used sweet cherry rootstocks (Gisela 6, Gisela 12, Krymsk 5, Colt, and Lanting) under prolonged natural heat stress. Morphological traits, leaf anatomical characteristics, antioxidant enzyme activities (SOD, CAT, POD), lipid peroxidation (MDA), phytohormones (ABA and JA), and osmotic regulators were assessed. Traits with high coefficients of variation, including POD activity, ABA, JA, and soluble protein content, were identified as sensitive indicators of heat stress. Lanting exhibited the strongest heat tolerance, characterized by thicker leaves, fewer heat-induced lesions, and enhanced antioxidant capacity, whereas Gisela 6 showed severe leaf abscission, elevated MDA and ABA accumulation, and the weakest defense capacity. Correlation analysis indicated that root sucker number was positively associated with SOD activity and soluble sugar content, suggesting a potential role of whole-plant carbon allocation in mitigating oxidative stress. Using the Entropy Weight–TOPSIS model, we provided a robust ranking that identifies Lanting and Colt as superior heat-resilient genotypes. The results provide a field-validated framework that bridges the gap between controlled-environment theory and practical orchard management, offering critical guidance for expanding sweet cherry cultivation into high-temperature regions.

DNA methylation is a conserved and vital epigenetic modification that plays essential roles in plant growth, development, and responses to environmental stress. Cytosine-5 DNA methyltransferases (C5-MTases) and DNA demethylases (dMTases) are key regulators of DNA methylation dynamics. However, a comprehensive characterization of these gene families in sweet potato has remained elusive. In this study, we systematically identified and analyzed eight C5-MTase and five dMTase genes in the genomes of diploid (Ipomoea trifida, 2n = 2x = 30) and autohexaploid (Ipomoea batatas, 2n = 6x = 90) sweet potato. Phylogenetic, structural, and synteny analyses revealed a high degree of conservation among these genes, suggesting their essential roles during evolution. Promoter analysis uncovered multiple cis-acting elements, particularly those responsive to light and hormones. In addition, we examined the expression profiling of IbC5-MTases and IbdMTases genes during storage root development, revealing that several were highly expressed during the early and rapid expansion stages. These findings suggest that C5-MTases and dMTases may contribute to the regulation of storage root formation in sweet potato through epigenetic mechanisms, offering valuable insights for future functional studies and epigenetic breeding efforts.

Melatonin (MT) has been widely recognized for its ability to mitigate the effects of abiotic stress and regulate plant development. In this study, we investigated the role of exogenous MT in enhancing heat tolerance in sweet potato, with a particular focus on its capacity to alleviate heat stress-induced damage. MT treatment significantly reduced oxidative stress, as evidenced by decreased levels of hydrogen peroxide, superoxide ions, and malondialdehyde (MDA), all of which were elevated under heat stress. To uncover the underlying mechanisms, RNA sequencing was performed on three experimental groups: control (CK), heat stress alone (HS), and MT pre-treatment followed by heat stress (MH). A total of 3491, 3280, and 1171 differentially expressed genes (DEGs) were identified in the CK vs. HS, CK vs. MH, and HS vs. MH comparisons, respectively. MT treatment notably modulated the expression of genes involved in redox regulation and nicotinate and nicotinamide metabolism. Moreover, MT enhanced the expression of genes associated with key signaling pathways, including mitogen-activated protein kinases (MPK3) and plant hormone signal transduction components, such as ethylene response factor (ERF). These findings offer novel insights into the mechanisms by which exogenous MT enhances heat tolerance in sweet potato, highlighting its role in regulating antioxidant systems, metabolic pathways, and hormone signaling. This study presents valuable strategies for improving crop resilience to heat stress.

Topping eliminates apical dominance in tobacco, enhancing the quality of the upper leaves. However, the mechanisms by which topping influences photosynthesis and the leaf structure, and regulation of chemical composition remain unclear. This study investigated the regulatory mechanisms of different topping periods (buttoning, budding, first flower, and full flower topping and without topping) on photosynthesis, the leaf structure, and the chemical composition in tobacco by integrating photosynthetic physiology, anatomical, and chemical composition analyses. The results indicated that topping makes the leaves thinner, promotes leaf lamina opening, and results in thicker mesophyll, compact palisade tissue, and loose spongy tissue. It can also significantly enhance photosynthetic capacity. The contents of total sugar, reducing sugar, and K2O content increased significantly, while the content of chloride ions decreased significantly. The contents of total nitrogen and nicotine were moderate. In conclusion, topping promotes leaf lamina opening, enhances photosynthesis, and associated with changes in the chemical composition of tobacco leaves. Additionally, this study aims to provide a theoretical basis for the promotion of tobacco topping techniques.

Tobacco (Nicotiana tabacum L.) is one of the world’s most economically important crops, with nicotine content being a crucial factor in determining its quality and economic value. By integrating plant physiology with transcriptomics and metabolomics analyses, we gained insight into the regulation of nicotine synthesis and metabolism in tobacco seedlings under different forms of nitrogen supply. Our findings revealed that ammonium nitrogen promotes nitrogen transformation in the root system of tobacco seedlings but inhibits root growth, whereas nitrate nitrogen inhibits biochemical processes but enhances root growth. Additionally, we observed that nitrate nitrogen facilitates the NAD + pathway in nicotine biosynthesis but inhibits the polyamine pathway, whereas ammonium nitrogen has the opposite effect. Overall, our comprehensive analysis indicates that the co-application of ammonium nitrate is conducive to nicotine synthesis. These results not only contribute to identifying key genes and metabolites involved in nicotine synthesis, but also provide a theoretical basis for establishing efficient regulation theories and pathways for tobacco's nitrogen utilization. Furthermore, they offer scientific support for future efforts aimed at regulating tobacco nicotine synthesis.

Merremia boisiana, a captivating species endemic to tropical rainforest habitats, belongs to the esteemed Convolvulaceae family. Renowned for its dazzling golden flowers and exceptional growth rate. This plant rapidly expands, covering other vegetation, suppressing the growth of native species, and altering light availability and nutrient distribution within the forest, thereby impacting ecological balance. Here, we report the first high-quality M. boisiana genome assembly, comprising 510 Mb with a contig N50 of 21 Mb and an assembly completeness of 98.7%. This assembly includes the identification of 15 chromosomes and the annotation of 37,389 protein-coding genes, with a high annotation rate of 99.2%. By integrating genomic data from other Convolvulaceae species, we analyzed the karyotype evolution of M. boisiana and uncovered the fundamental ploidy level of the Convolvulaceae family. Based on existing research, we identified 110 highly expressed genes involved in the biosynthesis of SA, IAA, JA, and ABA, all of which play essential roles in plant growth. The EPS1 transcription factor, involved in SA synthesis, along with YUC11 and TIR2, which participate in auxin biosynthesis, and OPR2, associated with ABA biosynthesis, collectively contribute to the enhanced root growth of M. boisiana through mechanisms such as gene expansion, gene dosage, and root-specific expression. This study not only sheds light on the genetic complexity of M. boisiana but also provides a promising direction for improving stress resistance in sweet potatoes and advancing ecological research. Our findings promote the sustainable utilization of this species while broadening our understanding of tropical plant genomics.

Leaf color mutants are valuable resources for studying photosynthesis, pigment metabolism, and gene regulatory networks in plants. In this study, a naturally occurring sweetpotato albino mutant exhibiting a stable white-leaf phenotype across developmental stages was identified and compared with its green-leaf wild type to elucidate the molecular mechanisms underlying albinism. The mutant showed a dramatic 98.8% reduction in total chlorophyll content and a markedly decreased Fv/Fm value (0.59), indicating severe impairment of PSII efficiency. Integrated transcriptomic analysis identified 3520 differentially expressed genes (DEGs), while metabolomic profiling revealed 270 differentially accumulated metabolites (DAMs). Genes involved in chlorophyll and carotenoid biosynthesis, chloroplast development, and photosynthetic electron transport were strongly repressed, including key regulators such as GLK1, PORA, and PORB. Metabolomic alterations were mainly enriched in flavonoids, phenylpropanoids, and amino acid-derived pathways, reflecting broad reprogramming of both primary and secondary metabolism. These changes were accompanied by severely disrupted chloroplast ultrastructure, suggesting a primary defect in plastid development. Collectively, the integrated multi-omics evidence provides a comprehensive understanding of the coordinated transcriptional and metabolic alterations driving the albino phenotype in sweetpotato and establishes this mutant as a potential model for studying the interplay between chloroplast biogenesis, photosynthesis, and secondary metabolism.

Tobacco is one of the most important model plants. Plant height is one of the most important agronomic traits in tobacco. To better understand the population genetic structure and the genetic basis of plant height in tobacco, 437 tobacco germplasms were whole genome re-sequencing in this study. A total of 2,263,775 high-quality single nucleotide polymorphisms were identified. The analysis of the population genetic structure showed that tobacco germplasm could be divided into 8 clusters. In addition, gene flow was found between flue-cured tobacco and ustic tobacco, as well as between oriental tobacco and air-cured tobacco. Three genes associated with plant height were identified as candidate genes by genome-wide association study. This study provides valuable genetic resources for population structure analysis and elucidation of the genetic basis of various traits. It helps to improve the efficiency of molecular breeding.

Salt stress profoundly impacts sweetpotato production. Exogenous glutathione (GSH) and melatonin (MT) promoted plant growth under stress, but their specific roles and mechanisms in sweetpotato salt tolerance need exploration. This study investigated GSH and MT’s regulatory mechanisms in sweetpotato under salt stress. Salt stress significantly reduces both growth and biomass by hindering photosynthesis, root traits, K+ content, and K+/Na+ balance, leading to oxidative stress and excessive hydrogen peroxide (H2O2), superoxide ion (O2•−), and malondialdehyde (MDA) production and Na+ accumulation. Nevertheless, GSH (2 mM) and MT (25 μM) pre-treatments effectively mitigated salt-induced oxidative damage and protected the plasma membrane. They reduced osmotic pressure by enhancing K+ uptake, K+/Na+ regulation, osmolyte accumulation, and reducing Na+ accumulation. Improved stomatal traits, chloroplast and grana lamella preservation, and maintenance of mesophyll cells, cell wall, and mitochondrial structure were observed with GSH and MT pre-treatments under salt stress, therefore boosting the photosynthetic system and enhancing plant growth and biomass. Moreover, the findings also indicate that the positive outcomes of GSH and MT pre-treatments result from elevated antioxidant levels, enhanced enzymatic activity, and upregulated expression of sodium hydrogen exchanger 2 (NHX2), K+ transporter 1 (AKT1), and cation/H+ exchanger (CHX), CBL-interacting protein kinase 1 (CIPK1), and antioxidant enzyme genes. These mechanisms enhance structural stability in photosynthesis and reduce salt stress. Evidently, MT pre-treatment exhibited superior effects compared to GSH. These findings provide a firm theoretical basis for employing GSH and MT to enhance salt tolerance in sweetpotato cultivation.

Abstract Background The 12-oxo-phytodienoic acid reductase (OPR) enzyme is crucial for the synthesis of jasmonates (JAs), and is involved in the plant stress response. However, the OPR gene family in sweetpotato, an important horticultural crop, remains unidentified. Results In this study, we employed bioinformatics techniques to identify nine IbOPR genes. Phylogenetic analysis revealed that these genes could be divided into Group I and Group II. Synteny analysis indicated that IbOPR evolution was driven by tandem duplication, whole-genome duplication (WGD), and segmental duplication events. The promoter sequences of IbOPRs were found to be associated with stress and hormonal responses. Additionally, we successfully cloned four IbOPRs from "Haida HD7791" and "Haida HD7798" using homologous cloning technology. These sequences were 1203 bp, 1200 bp, 1134 bp, and 1137 bp in length and encoded 400, 399, 377, and 378 amino acids, respectively. The protein sequence similarity between the salt-tolerant variety "Haida HD7791" and the salt-sensitive variety "Haida HD7798" was determined to be 96.75% for IbOPR2, 99.75% for IbOPR3, 92.06% for IbOPR6, and 98.68% for IbOPR7. Phylogenetic analysis categorized IbOPR2 and IbOPR3 proteins into Group II, while IbOPR6 and IbOPR7 proteins belonged to Group I. Subcellular localization experiments showed IbOPR2 protein present in the peroxisome, while IbOPR3, IbOPR6, and IbOPR7 proteins were found in the cytoplasm and nucleus. Salt stress induction experiments demonstrated that IbOPR2, IbOPR3, and IbOPR7 were significantly upregulated only in 'Haida HD7791' after 6 h. In contrast, IbOPR6 was induced in 'Haida HD7798' at 6 h but inhibited in 'Haida HD7791' at later time points (12, 24, 48, and 72 h), highlighting functional differences in salt stress responses. Conclusions Our findings suggest that IbOPR2 may play a crucial role in sweetpotato's response to salt stress by participating in JAs synthesis. These results provide a foundation for future functional analyses of OPR genes in sweetpotato.

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To characterize volatile organic compounds (VOCs) and aromatic sensory properties in Yun cigar, 27 samples from four origins were analyzed using SPME-HS-GC/MS and sensory analysis. The investigation results were analyzed using principal component analysis (PCA), Fisher linear discriminant analysis (LDA), and Pearson correlation analysis. In Yunnan cigars, the content of nicotine and neophytadiene accounted for over 90% of the total VOC content. Nicotine was significantly positively correlated with neophytadiene and phytol. The cigars from four origins were clearly classified by the PCA of VOCs. Four region discrimination functions were established through the LDA of 14 compounds, and the validation accuracy was 100%. The sensory descriptors with the highest geometric mean were woody, roasted, fresh-sweet, bean, and scorched. Acetophenone, megastigmatrienone A, and thunbergene were positively correlated with multiple aroma descriptors, while nicotine was negatively correlated with multiple aroma descriptors.

Japanese apricot is an important subtropical deciduous fruit tree in China, widely distributed in different altitude areas. How does it adapt to the different temperature environments in these areas? In this study, we identified a low-temperature transcription factor PmCBF03 on chromosome 7 through adaptive analysis of populations at different altitudes, which has an early termination single nucleotide polymorphism mutation. There were two different types of variation, PmCBF03A type in high-altitude areas and PmCBF03T type in low-altitude areas. PmCBF03A gene increased the survival rate, Fv/Fm values, antioxidant enzyme activity, and expression levels of antioxidant enzyme genes, and reducing electrolyte leakage and accumulation of reactive oxygen species in transgenic Arabidopsis under low temperature and freezing stress. Simultaneously, PmCBF03A gene promoted the dormancy of transgenic Arabidopsis seeds than wild-type. Biochemical analysis demonstrated that PmCBF03A directly bound to the DRE/CRT element in the promoters of the PmCOR413, PmDAM6 and PmABI5 genes, promoting their transcription and enhanced the cold resistance and dormancy of the overexpressing PmCBF03A lines. While PmCBF03T gene is unable to bind to the promoters of PmDAM6 and PmABI5 genes, leading to early release of dormancy to adapt to the problem of insufficient chilling requirement in low-altitude areas.

Somatic mutations arise and accumulate during tissue culture and vegetative propagation, potentially affecting various traits in horticultural crops, but their characteristics are still unclear. Here, somatic mutations in regenerated woodland strawberry derived from tissue culture of shoot tips under different conditions and 12 cultivated strawberry individuals are analyzed by whole genome sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 × 10-8-3.0 × 10-6 mutations per site. CG methylation shows a stable reduction (0.71%-8.03%) in regenerated plants, and hypoCG-DMRs are more heritable after sexual reproduction. A high-quality haplotype-resolved genome is assembled for the strawberry cultivar "Beni hoppe." The 12 "Beni hoppe" individuals randomly selected from different locations show 4731-6005 mutations relative to the reference genome, and the mutation frequency varies among the subgenomes. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale and nucleotide resolution in plants.

Dioscorea cirrhosa L. (D. cirrhosa) tuber is a traditional medicinal plant that is abundant in various pharmacological substances. Although diosgenin is commonly found in many Dioscoreaceae plants, its presence in D. cirrhosa remained uncertain. To address this, HPLC-MS/MS analysis was conducted and 13 diosgenin metabolites were identified in D. cirrhosa tuber. Furthermore, we utilized transcriptome data to identify 21 key enzymes and 43 unigenes that are involved in diosgenin biosynthesis, leading to a proposed pathway for diosgenin biosynthesis in D. cirrhosa. A total of 3,365 unigenes belonging to 82 transcription factor (TF) families were annotated, including MYB, AP2/ERF, bZIP, bHLH, WRKY, NAC, C2H2, C3H, SNF2 and Aux/IAA. Correlation analysis revealed that 22 TFs are strongly associated with diosgenin biosynthesis genes (—r2— > 0.9, P < 0.05). Moreover, our analysis of the CYP450 gene family identified 206 CYP450 genes (CYP450s), with 40 being potential CYP450s. Gene phylogenetic analysis revealed that these CYP450s were associated with sterol C-22 hydroxylase, sterol-14-demethylase and amyrin oxidase in diosgenin biosynthesis. Our findings lay a foundation for future genetic engineering studies aimed at improving the biosynthesis of diosgenin compounds in plants.

Potassium ion (K+) is one of the most essential nutrients for the growth and development of tobacco (Nicotiana tabacum L.), however, the molecular regulation of K+ concentration in tobacco remains unclear. In this study, a two-pore K (TPK) channel gene NtTPKa was cloned from tobacco, and NtTPKa protein contains the unique K+ selection motif GYGD and its transmembrane region primarily locates in the tonoplast membrane. The expression of NtTPKa gene was significantly increased under low-potassium stress conditions. The concentrations of K+ in tobacco were significantly increased in the NtTPKa RNA interference lines and CRISPR/Cas9 knockout mutants. In addition, the transport of K+ by NtTPKa was validated using patch clamp technique, and the results showed that NtTPKa channel protein exclusively transported K+ in a concentration-dependent manner. Together, our results strongly suggested that NtTPKa is a key gene in maintaining K+ homeostasis in tobacco, and it could provide a new genetic resource for increasing the concentration of K+ in tobacco.