Transcriptome Analysis Reveals the Different Response to Toxic Stress in Rootstock Grafted and Non-Grafted Cucumber Seedlings

Silicon-seed priming promotes seed germination under CA-induced autotoxicity by improving sucrose and respiratory metabolism in cucumber (Cucumis sativus L.)

Seed germination is one of the critical and sensitive stages of early plant growth, and its process is prevented by cinnamic acid (CA). Silicon (Si) plays a critical role in mitigating abiotic stresses and seed germination in plants, but little is known about its role in seed germination and physiology in CA-stressed cucumber. Here, we conducted experiments in the State Key Laboratory of Aridland Crop Science, Gansu Agricultural University from March to June 2021 to investigate the effects of Si-seed priming on growth, antioxidant capacity, sucrose mobilization and respiratory metabolism during germination under CA stress. Our results showed that seed soaking with Si (9 mmol/L) significantly reduced membrane lipid peroxidation and promoted post-germination growth of cucumber seeds under CA (2.0 mmol/L) stress. Si increased key enzyme activities in sucrose metabolism in CA-stressed seeds after germination, accelerating sucrose degradation and fructose synthesis. Si also enhanced the activities of key enzymes in the glycolytic pathway and pentose phosphate pathway in seeds, as well as in the post-germination tricarboxylic acid cycle, promoting glucose decomposition and ATP synthesis. Principal component analysis significantly separated the CK, Si, and CA + Si treatments from the CA treatment in the first principal component after 48 h of treatment. In addition, qRT-PCR analysis showed that Si induced overexpression of genes related to sucrose and respiratory metabolism in seeds treated with CA for 48 h. In conclusion, our findings provide evidence that Si priming may be an effective method to reverse CA inhibition of cucumber seeds, which effectively improve germination under CA stress by attenuating membrane lipid peroxidation and enhancing sucrose mobilization and respiratory metabolism in cucumber.

Accumulation patterns of tobacco root allelopathicals across different cropping durations and their correlation with continuous cropping challenges

Introduction

Continuous cropping challenges have gradually emerged as pivotal factors limiting the sustainable development of agricultural production. Allelopathicals are considered to be the primary obstacles. However, there is limited information on allelopathic accumulation across various continuous cropping years and its correlation with the associated challenges.

Methods

Tobacco was subjected to varying planting durations: 1 year (CR), 5 years (CC5), 10 years (CC10), and 15 years (CC15).

Results

Our findings unveiled discernible disparities in tobacco growth patterns across diverse continuous cropping periods. Notably, the most pronounced challenges were observed in the CC5 category, characterized by yield reduction, tobacco black shank outbreaks, and a decline in beneficial flora. Conversely, CC15 exhibited a substantial reduction in challenges as the continuous cropping persisted with no significant differences when compared to CR. Within the tobacco rhizosphere, we identified 14 distinct allelopathic compounds, with 10 of these compounds displaying noteworthy variations among the four treatments. Redundancy analysis (RDA) revealed that eight allelopathic compounds exhibited autotoxic effects on tobacco growth, with MA, heptadecanoic acid, and VA ranking as the most potent inhibitors. Interaction network highlighted the pivotal roles of VA and EA in promoting pathogen proliferation and impeding the enrichment of 13 beneficial bacterial genera. Furthermore, a structural equation model elucidated that MA and EA primarily exert direct toxic effects on tobacco, whereas VA fosters pathogen proliferation, inhibits the enrichment of beneficial bacteria, and synergistically exacerbates the challenges associated with continuous cropping alongside EA.

Discussion

These findings suggested discernible disparities in tobacco growth patterns across the various continuous cropping periods. The most pronounced challenges were observed in CC5, whereas CC15 exhibited a substantial reduction in challenges as continuous cropping persisted. VA may play a pivotal role in this phenomenon by interacting with pathogens, beneficial bacterial genera, and EA.

Time-course adaptive changes in hippocampal transcriptome and synaptic function induced by simulated microgravity associated with cognition

Introduction

The investigation of cognitive function in microgravity, both short-term and long-term, remains largely descriptive. And the underlying mechanisms of the changes over time remain unclear.

Methods

Behavioral tests, electrophysiological recording, and RNA sequencing were used to observe differences in behavior, synaptic plasticity, and gene expression.

Results

Initially, we measured the performance of spatial cognition exposed to long-term simulated microgravity (SM). Both working memory and advanced cognitive abilities were enhanced. Somewhat surprisingly, the synaptic plasticity of the hippocampal CA3-CA1 synapse was impaired. To gain insight into the mechanism of changing regularity over time, transcriptome sequencing in the hippocampus was performed. The analysis identified 20 differentially expressed genes (DEGs) in the hippocampus after short-term modeling, 19 of which were up-regulated. Gene Ontology (GO) analysis showed that these up-regulated genes were mainly enriched in synaptic-related processes, such as Stxbp5l and Epha6. This might be related to the enhancement of working memory performance under short-term SM exposure. Under exposure to long-term SM, 7 DEGs were identified in the hippocampus, all of which were up-regulated and related to oxidative stress and metabolism, such as Depp1 and Lrg1. Compensatory effects occurred with increased modeling time.

Discussion

To sum up, our current research indicates that the cognitive function under SM exposure is consistently maintained or potentially even being enhanced over both short and long durations. The underlying mechanisms are intricate and potentially linked to the differential expression of hippocampal-associated genes and alterations in synaptic function, with these effects being time-dependent. The present study will lay the experimental and theoretical foundation of the multi-level mechanism of cognitive function under space flight.

Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches

Abiotic stress in cucumber (Cucumis sativus L.) may trigger distinct transcriptome responses, resulting in significant yield loss. More insight into the molecular underpinnings of the stress response can be gained by combining RNA-Seq meta-analysis with systems biology and machine learning. This can help pinpoint possible targets for engineering abiotic tolerance by revealing functional modules and key genes essential for the stress response. Therefore, to investigate the regulatory mechanism and key genes, a combination of these approaches was utilized in cucumber subjected to various abiotic stresses. Three significant abiotic stress-related modules were identified by gene co-expression network analysis (WGCNA). Three hub genes (RPL18, δ-COP, and EXLA2), ten transcription factors (TFs), one transcription regulator, and 12 protein kinases (PKs) were introduced as key genes. The results suggest that the identified PKs probably govern the coordination of cellular responses to abiotic stress in cucumber. Moreover, the C2H2 TF family may play a significant role in cucumber response to abiotic stress. Several C2H2 TF target stress-related genes were identified through co-expression and promoter analyses. Evaluation of the key identified genes using Random Forest, with an area under the curve of ROC (AUC) of 0.974 and an accuracy rate of 88.5%, demonstrates their prominent contributions in the cucumber response to abiotic stresses. These findings provide novel insights into the regulatory mechanism underlying abiotic stress response in cucumber and pave the way for cucumber genetic engineering toward improving tolerance ability under abiotic stress.

Biochar-Dual Oxidant Composite Particles Alleviate the Oxidative Stress of Phenolic Acid on Tomato Seed Germination

Phenolic acid is a well-known allelochemical, but also a pollutant in soil and water impeding crop production. Biochar is a multifunctional material widely used to mitigate the phenolic acids allelopathic effect. However, phenolic acid absorbed by biochar can still be released. In order to improve the removal efficiency of phenolic acids by biochar, the biochar-dual oxidant (BDO) composite particles were synthesized in this study, and the underlying mechanism of the BDO particles in ameliorating p-coumaric acid (p-CA) oxidative damage to tomato seed germination was revealed. Upon p-CA treatment, the BDO composite particles application increased the radical length, radical surface area, and germination index by 95.0%, 52.8%, and 114.6%, respectively. Compared to using biochar or oxidants alone, the BDO particles addition resulted in a higher removal rate of p-CA and produced more O₂^•-, HO^•, SO₄^•- and ¹O₂ radicals via autocatalytic action, suggesting that BDO particles removed phenolic acid by both adsorption and free radical oxidation. The addition of BDO particles maintained the levels of the antioxidant enzyme activity close to the control, and reduced the malondialdehyde and H₂O₂ by 49.7% and 49.5%, compared to the p-CA treatment. Integrative metabolomic and transcriptomic analyses revealed that 14 key metabolites and 62 genes were involved in phenylalanine and linoleic acid metabolism, which increased dramatically under p-CA stress but down-regulated with the addition of BDO particles. This study proved that the use of BDO composite particles could alleviate the oxidative stress of phenolic acid on tomato seeds. The findings will provide unprecedented insights into the application and mechanism of such composite particles as continuous cropping soil conditioners.

Comparative Transcriptomic and Physiological Analyses Reveal Key Factors for Interstocks to Improve Grafted Seedling Growth in Tangor

Interstock is an important agronomic technique for regulating plant growth and fruit quality, and overcoming the incompatibility between rootstocks and scions; however, the underlying mechanisms remain largely unknown. In this study, the effects and regulatory mechanisms of tangor grafting, with and without interstocks, on the growth and development of scions were analyzed by combining morphology, physiology, anatomy and transcriptomics. Morphological and physiological analyses showed that interstocks ('Aiyuan 38' and 'Daya') significantly improved the growth of seedlings, effectively enhanced the foliar accumulation of chlorophyll and carotenoids, and increased the thickness of leaf tissues. Using 'Aiyuan 38' as the interstock, photosynthetic efficiency and starch content of citrus seedlings improved. Transcriptomics showed that genes related to photosynthesis and photosynthetic antenna proteins were upregulated in interstock-treated seedlings, with significant upregulation of photosystem PSI- and PSII-related genes. In addition, multiple key genes may be involved in plant hormone signaling, starch and sucrose metabolism, and transcriptional regulation. Taken together, these findings provide novel insights into the role of interstocks in regulating and contributing to the growth and development of grafted seedlings, and will further define and deploy candidate genes to explore the mechanisms of rootstock-interstock-scion interactions.

Insights into the impacts of autotoxic allelochemicals from rhizosphere of Atractylodes lancea on soil microenvironments

Atractylodes lancea suffers from continuous cropping obstacles that have become a major constraint in its cultivation, but there is still little information on the autotoxic allelochemicals and their interaction with soil microorganisms. In this study, we firstly identified the autotoxic allelochemicals from rhizosphere of A. lancea and determined their autotoxicity. Third-year continuous A. lancea cropping soils, i.e., rhizospheric soil and bulk soil, compared with control soil and one-year natural fallow soil were used to determine soil biochemical properties and microbial community. Eight allelochemicals from A. lancea roots were detected and exhibited significant autotoxicity effects on seed germination and seedling growth of A. lancea with the highest content of dibutyl phthalate in rhizospheric soil and lowest IC₅₀ value of 2,4-di-tert-butylphenol inhibiting seed germination. The contents of soil nutrients and organic matter, pH value, and enzyme activity were altered between different soils, and the parameters of fallow soil were close to those of the unplanted soil. The PCoA analysis indicated that the community composition of both bacteria and fungi were differed significantly among the soil samples. Continuous cropping decreased OTUs numbers of bacterial and fungal communities, and natural fallow restored them. The relative abundance of Proteobacteria, Planctomycetes, and Actinobacteria decreased, and that of Acidobacteria and Ascomycota increased after three years cultivation. The LEfSe analysis identified 115 and 49 biomarkers for bacterial and fungal communities, respectively. The results suggested that natural fallow restored the structure of soil microbial community. Overall, our results revealed that autotoxic allelochemicals caused the variations of soil microenvironments and resulted in replantation problem of A. lancea, and natural fallow alleviated the soil deterioration by remodeling the rhizospheric microbial community and restoring soil biochemical properties. These findings provide important insights and clues for solving the continuous cropping problems and guiding the management of sustainable farmland.

Response of Cucumis sativus to Neighbors in a Species-Specific Manner

Plants exhibit various behaviors of growth and allocation that play an important role in plant performance and social interaction as they grow together. However, it is unclear how Cucumis sativus plants respond to different neighbors. Here, we performed 5 neighbor combinations with C. sativus as the focal species. The selected materials of C. sativus responded to neighbors and exhibited different behavior strategies in a species-specific manner. All competition treatments reduced the growth of C. sativus seedlings to a certain extent, but only the Eruca sativa neighbor treatment reached a significant level in total root length and shoot biomass. Compared with growing under solitary conditions, focal plants avoided, tended to and did not change their allocation to their nearby plants. The larger the biomass of their neighbors, the stronger the inhibition of the focal plants. In addition, no significant correlations between growth and allocation variables were found, suggesting that growth and allocation are two important aspects of C. sativus behavioral strategies. Our findings provide reference and support for agricultural production of C. sativus, but further research and practice are still needed.

Combined physiological and transcriptome analysis revealed the response mechanism of Pogostemon cablin roots to p-hydroxybenzoic acid

Pogostemon cablin (patchouli) cultivation is challenged by serious soil sickness, of which autotoxins accumulation is a major cause. p-hydroxybenzoic acid (p-HBA) is one of the main autotoxins of patchouli. However, the molecular mechanism underlying the response of patchouli to p-HBA remains unclear. In this study, RNA-sequencing combined with physiological analysis was used to monitor the dynamic transcriptomic and physiological changes in patchouli seedlings 0, 6, 12, 24, 48, and 96 h after p-HBA treatment. p-HBA stress inhibited root biomass accumulation, induced excessive hydrogen peroxide accumulation and lipid peroxidation, and activated most antioxidant enzymes. Compared with that of the control, the osmotic adjustment substance content was elevated with treatment. Subsequently, 15,532, 8,217, 8,946, 2,489, and 5,843 differentially expressed genes (DEGs) at 6, 12, 24, 48, and 96 h after p-HBA treatment, respectively, were identified in patchouli roots. GO functional enrichment analysis showed that the DEGs were enriched mainly in plasma membrane, defense response, response to chitin, DNA-binding transcription factor activity and abscisic acid-activated signaling pathway. The upregulated genes were involved in glycolysis/gluconeogenesis, cysteine and methionine metabolism, starch and sucrose metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid metabolism. Genes associated with MAPK signaling pathway-plant, plant-pathogen interaction, plant hormone signal transduction were downregulated with p-HBA treatment. These pathways are related to root browning and rotting, leading to plant death.

Exogenous silicon alleviates the adverse effects of cinnamic acid-induced autotoxicity stress on cucumber seedling growth

Autotoxicity is a key factor that leads to obstacles in continuous cropping systems. Although Si is known to improve plant resistance to biotic and abiotic stresses, little is known about its role in regulating leaf water status, mineral nutrients, nitrogen metabolism, and root morphology of cucumber under autotoxicity stress. Here, we used cucumber seeds (Cucumis sativus L. cv. "Xinchun No. 4") to evaluate how exogenous Si (1 mmol L^-1) affected the leaf water status, mineral nutrient uptake, N metabolism-related enzyme activities, root morphology, and shoot growth of cucumber seedlings under 0.8 mmol L^-1 CA-induced autotoxicity stress. We found that CA-induced autotoxicity significantly reduced the relative water content and water potential of leaves and increase their cell sap concentration. CA-induced stress also inhibited the absorption of major (N, P, K, Ca, Mg) and trace elements (Fe, Mn, Zn). However, exogenous Si significantly improved the leaf water status (relative water content and water potential) of cucumber leaves under CA-induced stress. Exogenous Si also promoted the absorption of mineral elements by seedlings under CA-induced stress and alleviated the CA-induced inhibition of N metabolism-related enzyme activities (including nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase, glutamate dehydrogenase). Moreover, exogenous Si improved N uptake and utilization, promoted root morphogenesis, and increased the growth indexes of cucumber seedlings under CA-induced stress. Our findings have far-reaching implications for overcoming the obstacles to continuous cropping in cucumber cultivation.

Serial-Omics and Molecular Function Study Provide Novel Insight into Cucumber Variety Improvement

Cucumbers are rich in vitamins and minerals. The cucumber has recently become one of China’s main vegetable crops. More specifically, the adjustment of the Chinese agricultural industry’s structure and rapid economic development have resulted in increases in the planting area allocated to Chinese cucumber varieties and in the number of Chinese cucumber varieties. After complete sequencing of the “Chinese long” genome, the transcriptome, proteome, and metabolome were obtained. Cucumber has a small genome and short growing cycle, and these traits are conducive to the application of molecular breeding techniques for improving fruit quality. Here, we review the developments and applications of molecular markers and genetic maps for cucumber breeding and introduce the functions of gene families from the perspective of genomics, including fruit development and quality, hormone response, resistance to abiotic stress, epitomizing the development of other omics, and relationships among functions.

Grafting-enhanced tolerance of cucumber to toxic stress is associated with regulation of phenolic and other aromatic acids metabolism

Toxic stress caused by autotoxins is a common phenomenon for cucumber under monoculture condition. A previous study demonstrated that grafting could enhance the resistance of cucumber to cinnamic acid (CA) stress, but the underlying mechanism behind this enhanced resistance is still unclear. In the present study, we reconfirmed the stronger resistance of grafted rootstock (RG) compared to the non-grafted (NG) cucumber as measured though plant biomass accumulation. In addition, we focused on the phenolic and other aromatic acids metabolism in hydroponic culture model system using a combination of qRT-PCR (to measure gene expression of relevant genes) and HPLC (to detect the presence of phenolic and other aromatic acids). The results showed that the exogenous CA lead to the expression of four enzymes involved in phenolic and other aromatic acids biosynthesis, and a larger increase was observed in grafted rootstock (RG). Specifically, expression of six genes, involved in phenolic and other aromatic acids biosynthesis (PAL, PAL1, C4H, 4CL1, 4CL2 and COMT), with the exception of 4CL2, were significantly up-regulated in RG but down-regulated in NG when exposed to CA. Furthermore, six kinds of phenolic and other aromatic acids were detected in leaves and roots of NG and RG cucumber, while only benzoic acid and cinnamic acid were detected in root exudate of all samples. The CA treatment resulted in an increase of p-hydroxybenzonic acid, benzoic acid and cinnamic acid contents in RG cucumber, but decrease of p-coumaric acid and sinapic acid contents in NG cucumber. Surprisingly, the type and amount of phenolic and other aromatic acids in root exudate was improved by exogenous CA, particularly for RG cucumber. These results suggest that a possible mechanism for the stronger resistance to CA of RG than NG cucumber could involve the up-regulation of key genes involved in phenolic and other aromatic acids metabolism, and that the excessive phenolic compounds released to surroundings is a result of the accumulation of phenolic compounds in a short time by the plant under stress.

Can Grafting Manage Fusarium Wilt Disease of Cucumber and Increase Productivity under Heat Stress?

Cucumber production is considered a crucial problem under biotic and abiotic stress, particularly in arid and semi-arid zones. The current study investigated the impact of grafted cucumber plants on five cucurbit rootstocks under infection with Fusarium oxysporum f. sp. cucumerinum alone and in combination with heat stress in two different locations (i.e., Kafr El-Sheikh and Sidi Salem) during the year of 2021. The rootstock of VSS-61 F₁ displayed the highest level of resistance with values 20.8 and 16.6% for wilt incidence and 79.2 and 83.4% for the wilt reduction, respectively for both locations. This rootstock showed the lowest disease severity of fusarium wilt (15.3 and 12%), and high grafting efficiency (85 and 88%), respectively in both locations. Grafting also improved plant vigor and cucumber production under heat stress (40-43 °C). The rootstocks VSS-61 F₁, Ferro and Super Shintoza significantly increased the total yield of cucumber plants compared to non-grafted cucumber and the rootstock Bottle gourd in both locations. Further studies are needed on grafted plants under multiple stresses in terms of plant biological levels, including physiological, biochemical and genetic attributes.

Rootstock-scion exchanging mRNAs participate in the pathways of amino acids and fatty acid metabolism in cucumber under early chilling stress

Cucumber (Cucumis sativus L.) often experiences chilling stress that limits their growth and productivity. Grafting is widely used to improve abiotic stress resistance by alternating a vigorous root system, suggesting there exists systemic signals communication between distant organs. mRNAs are reported to be evolving in fortification strategies by long-distance signaling when plants suffering from chilling stress. However, the potential function of mobile mRNAs alleviating chilling stress in grafted cucumber is still unknown. Here, the physiological changes, mobile mRNAs profiling, transcriptomic and metabolomic changes in above- and underground tissues of all graft combinations of cucumber and pumpkin responding to chilling stress were established and analyzed comprehensively. The co-relationship between the cluster of chilling-induced pumpkin mobile mRNAs with Differentially Expressed Genes (DEGs) and Differentially Intensive Metabolites (DIMs) revealed that four key chilling-induced pumpkin mobile mRNAs were highly related to glycine, serine and threonine synthesis and fatty acid β-oxidative degradation metabolism in cucumber tissues of heterografts. The verification of mobile mRNAs, potential transport of metabolites and exogenous application of key metabolites of glycerophospholipid metabolism pathway in cucumber seedlings confirmed that the role of mobile mRNAs in regulating chilling responses in grafted cucumber. Our results build a link between the long-distance mRNAs of chilling-tolerant pumpkin and the fatty acid β-oxidative degradation metabolism of chilling-sensitive cucumber. It helps to uncover the mechanism of signaling interaction between scion and stock responding to chilling tolerant in grafted cucumber.

Exogenous silicon enhances the systemic defense of cucumber leaves and roots against CA-induced autotoxicity stress by regulating the ascorbate-glutathione cycle and photosystem II

Cinnamic acid (CA), one of the main autotoxins secreted by cucumber roots during continuous cropping, inhibits plant growth and reduces yield. Silicon (Si) is an environmentally friendly element that alleviates abiotic stresses in plants, but the mechanism underlying its resistance to autotoxicity remain unclear. Here, we used 0.8 mmol L^-1 CA to study the effects of Si application on the growth, chlorophyll fluorescence, and ascorbate-glutathione (AsA-GSH) cycle of cucumber seedlings under CA inducing conditions. Our results indicated that CA significantly induced photoinhibition and overaccumulation of reactive oxygen species (ROS), thereby inhibiting cucumber growth. Treatment with 1.0 mmol L^-1 Si improved plant height, stem diameter and biomass accumulation, and protected the photosynthetic electron transport function of photosystem II in the presence of CA. Similarly, Si application maintained the ROS status by increasing ascorbate (AsA) and glutathione (GSH) production, as well as the ratios of AsA/DHA and GSH/GSSG in both leaves and roots during CA stress. In addition, Si application in CA-treated seedlings enhanced the activity of key enzymes such as ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione S-transferase (GST), and the transcription of several enzyme genes (CsAPX, CsMDHAR and CsGR） from the AsA-GSH cycle. These results suggest that exogenous Si enhances CA tolerance in cucumber seedlings by protecting photosystem II activity, upregulating AsA-GSH pathway, and reducing ROS levels.

Genetic transformation and growth index determination of the Larix olgensis LoHDZ2 transcription factor gene in tobacco

Homeodomain-leucine zippers (HD-Zip) are plant-specific transcription factors that participate in different plant development processes and differentially regulate metabolic processes. LoHDZ2 is an HD-ZipII subfamily transcription factor gene that we identified from a transcriptomic analysis of Larix olgensis. To understand its function, we built a LoHDZ2 expression vector and then inserted it into tobacco by genetic transformation. Transgenic plants were identified at the DNA and RNA levels. Phenotypic index analysis of transgenic tobacco showed dwarfed growth with larger leaves and earlier flowering than the wild type. LoHDZ2 was expressed differently after hormone treatment with IAA, MeJA and 2,4-D. The results suggested that LoHDZ2 may respond to hormones and be involved in regulating growth and metabolism. These results helped us better understand the function of LoHDZ2 and provided a candidate gene for Larix olgensis molecular breeding.