Influence of graphene on the multiple metabolic pathways of Zea mays roots based on transcriptome analysis

Global Transcriptomic Analysis of Inbred Lines Reveal Candidate Genes for Response to Maize Lethal Necrosis

Maize lethal necrosis (MLN) is a significant threat to food security in Sub-Saharan Africa (SSA), with limited commercial inbred lines displaying tolerance. This study analyzed the transcriptomes of four commercially used maize inbred lines and a non-adapted inbred line, all with varying response levels to MLN. RNA-Seq revealed differentially expressed genes in response to infection by maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV), the causative agents of MLN. Key findings included the identification of components of the plant innate immune system, such as differentially regulated R genes (mainly LRRs), and activation/deactivation of virus resistance pathways, including RNA interference (RNAi) via Argonaute (AGO), Dicer-like proteins, and the ubiquitin-proteasome system (UPS) via RING/U-box and ubiquitin ligases. Genes associated with redox signaling, WRKY transcription factors, and cell modification were also differentially expressed. Additionally, the expression of translation initiation and elongation factors, eIF4E and eIF4G, correlated with the presence of MLN viruses. These findings provide valuable insights into the molecular mechanisms of MLN resistance and highlight potential gene candidates for engineering or selecting MLN-resistant maize germplasm for SSA.

Time-Course Transcriptomics Analysis Reveals Molecular Mechanisms of Salt-Tolerant and Salt-Sensitive Cotton Cultivars in Response to Salt Stress

Salt stress is an environmental factor that limits plant seed germination, growth, and survival. We performed a comparative RNA sequencing transcriptome analysis during germination of the seeds from two cultivars with contrasting salt tolerance responses. A transcriptomic comparison between salt-tolerant cotton cv Jin-mian 25 and salt-sensitive cotton cv Su-mian 3 revealed both similar and differential expression patterns between the two genotypes during salt stress. The expression of genes related to aquaporins, kinases, reactive oxygen species (ROS) scavenging, trehalose biosynthesis, and phytohormone biosynthesis and signaling that include ethylene (ET), gibberellin (GA), abscisic acid (ABA), jasmonic acid (JA), and brassinosteroid (BR) were systematically investigated between the cultivars. Despite the involvement of these genes in cotton's response to salt stress in positive or negative ways, their expression levels were mostly similar in both genotypes. Interestingly, a PXC2 gene (Ghir_D08G025150) was identified, which encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). This gene showed an induced expression pattern after salt stress treatment in salt-tolerant cv Jin-mian 25 but not salt-sensitive cv Su-mian 3. Our multifaceted transcriptome approach illustrated a differential response to salt stress between salt-tolerant and salt-sensitive cotton.

Expression profile analysis of cotton fiber secondary cell wall thickening stage

To determine the genes associated with the fiber strength trait in cotton, three different cotton cultivars were selected: Sea Island cotton (Xinhai 32, with hyper-long fibers labeled as HL), and upland cotton (17-24, with long fibers labeled as L, and 62-33, with short fibers labeled as S). These cultivars were chosen to assess fiber samples with varying qualities. RNA-seq technology was used to analyze the expression profiles of cotton fibers at the secondary cell wall (SCW) thickening stage (20, 25, and 30 days post-anthesis (DPA)). The results showed that a large number of differentially expressed genes (DEGs) were obtained from the three assessed cotton cultivars at different stages of SCW development. For instance, at 20 DPA, Sea Island cotton (HL) had 6,215 and 5,364 DEGs compared to upland cotton 17-24 (L) and 62-33 (S), respectively. Meanwhile, there were 1,236 DEGs between two upland cotton cultivars, 17-24 (L) and 62-33 (S). Gene Ontology (GO) term enrichment identified 42 functions, including 20 biological processes, 11 cellular components, and 11 molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified several pathways involved in SCW synthesis and thickening, such as glycolysis/gluconeogenesis, galactose metabolism, propanoate metabolism, biosynthesis of unsaturated fatty acids pathway, valine, leucine and isoleucine degradation, fatty acid elongation pathways, and plant hormone signal transduction. Through the identification of shared DEGs, 46 DEGs were found to exhibit considerable expressional differences at different fiber stages from the three cotton cultivars. These shared DEGs have functions including REDOX enzymes, binding proteins, hydrolases (such as GDSL thioesterase), transferases, metalloproteins (cytochromatin-like genes), kinases, carbohydrates, and transcription factors (MYB and WRKY). Therefore, RT-qPCR was performed to verify the expression levels of nine of the 46 identified DEGs, an approach which demonstrated the reliability of RNA-seq data. Our results provided valuable molecular resources for clarifying the cell biology of SCW biosynthesis during fiber development in cotton.

Graphene promotes the growth of Vigna angularis by regulating the nitrogen metabolism and photosynthesis

Graphene has promising applications in agriculture and forestry. In the current study, six different concentrations of graphene (0mg/L, 0.01mg/L, 0.10mg/L, 1.00mg/L, 10.00mg/L, and 100.00mg/L) were used to investigate its effect on the growth and development of V. angularis plants in soil culture. The results showed that the group treated with 1.00mg/L graphene (G-1) had significantly increased plant height (19.86%), stem diameter (24.33%), and leaf area (13.69%), compared to the control group (CK). Moreover, all concentrations of graphene had positive effects on the total root length, total root surface area, and the number of root tips of V. angularis. Compared to the CK group, the G-1 group had significantly increased leaf water potential (37.89%), leaf conductivity (2.25%), and SOD, POD, and CAT activities (47.67%, 35.22%, and 199.3%, respectively). The G-1 group also showed improved leaf net photosynthetic rate, chlorophyll content, and soluble sugar content (51.28%, 24.25%, and 38.35%, respectively), compared to the CK group. Additionally, 1.00mg/L graphene led to a 23.88% increase in the podding rate and a 17.04% increase in the yield of V. angularis plants. The rhizosphere soil of V. angularis treated with 1.00mg/L graphene had a 25.14% increase in hydrolyzable nitrogen content and a 66.67% increase in available phosphorus content. RNA-seq data indicated that 1.00mg/L graphene induced the expression of photosynthesis and nitrogen transmembrane transport genes, including ATP synthase subunit b, photosystem I reaction center subunit XI, photosystem I reaction center subunit IV A, ferredoxin, and psbP-like protein 1, as well as genes for photosynthesis antenna proteins, glutamine synthetase, glutamate dehydrogenase 1, cyanate hydratase, protein fluG-like, and NRT1/PTR family, suggesting that graphene promoted the growth and development of V. angularis by enhancing the photosynthesis and nitrogen metabolism processes in V. angularis plants. Our results indicated that a suitable concentration of graphene could significantly promote the growth of V. angularis plants in soil.

Graphene oxide influences transfer of plasmid-mediated antibiotic resistance genes into plants

As an emerging contaminant, antibiotic resistance genes (ARGs) are raising concerns about its significant threat to public health. Meanwhile, graphene oxide (GO), which also has a potential ecological damage with increasingly entering the environment, has a great influence on the transfer of ARGs. However, little is known about the effects mechanisms of GO on the migration of antibiotic resistance genes (ARGs) from bacteria into plants. In this study, we investigated the influence of GO on the transfer of ARGs carried by RP4 plasmids from Bacillus subtilis into rice plants. Our results showed that the presence of GO at concentrations ranging from 0 to 400 mg L-1 significantly reduced the transfer of ARGs into rice roots by 13-71 %. Moreover, the migration of RP4 from the roots to aboveground parts was significantly impaired by GO. These effects may be attributed to several factors. First, higher GO concentrations led to low pH in the culture solution, resulting in a substantial decrease in the number of antibiotic-resistant bacteria. Second, GO induced oxidative stress in rice, as indicated by enhanced Evans blue dye staining, and elevated levels of malondialdehyde, nitric oxide, and phenylalanine ammonia-lyase activity. The oxidative stress negatively affected plant growth, as demonstrated by the reduced fresh weight and altered lignin content in the rice. Microscopic observations confirmed the entry of GO into root cells but not leaf mesophyll cells. Furthermore, potential recipients of RP4 plasmid strains in rice after co-cultivation experiments were identified, including Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus cereus. These findings clarify the influence of GO on ARGs in the bacteria-plant system and emphasize the need to consider its potential ecological risks.

Graphene nanoparticles improve alfalfa (Medicago sativa L.) growth through multiple metabolic pathways under salinity-stressed environment

Graphene, one of the emerging carbon nanomaterials, has many advantages and applications. Salinity stress seriously affects ecology and agroforestry worldwide. The effects of graphene on alfalfa under salinity stress were investigated. The results indicated that graphene promoted alfalfa growth under non-salinity stress but caused some degree of damage to root cells and leaf parameters. Graphene used in salinity stress had a positive effect on growth parameters, chlorophyll, photosynthetic gas parameters, stomatal opening, ion balance, osmotic homeostasis, cell membrane integrity and antioxidant system, while it decreased Na+, lipid peroxidation and reactive oxygen species levels. Correlation analysis revealed that most of the parameters were significantly correlated; and principal component analysis indicated that the first two dimensions (78.1% and 4.1%) explained 82.2% of the total variability, and the majority of them exceeded the average contribution. Additionally, Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analysis showed that there were numerous differentially expressed genes and pathways to regulate alfalfa responding to salinity stress. Taken together, the findings reveal that graphene does not enter the plant, but improves the properties and adsorption of soil to enhance salt tolerance and seedling growth of alfalfa through morphological, physiological, biochemical, and transcriptomic aspects. Furthermore, this study provides a reference for the application of graphene to improve soil environment and agricultural production.

Unveiling the Effects of Carbon-Based Nanomaterials on Crop Growth: From Benefits to Detriments

To systematically assess the impact of typical CNMs on the growth effects of cereal crops, we conducted a meta-analysis of 48 independent studies worldwide. The pooled results showed that shoot weight (13.39%) and antioxidant metabolite content (SOD: 106.32%, POD: 32.29%, CAT: 22.63%) of cereal crops exposed to the presence of CNMs were significantly increased, but phytohormones secretion (17.84%) was inhibited. The results of subgroup analysis showed that there were differences in the results of different CNM types with the same exposure concentration on growth effects. Short-term exposure adversely affected the root and photosynthetic capacity of the crop, but prolonged exposure instead showed a promoting effect. Multiple linear regression analysis showed that the concentration of CNMs and cereal variety variables were significantly associated with changes in multiple growth effect values. This work could offer references and fresh perspectives for investigating how nanoparticles and crops interact.

Effects of concentration-dependent graphene on maize seedling development and soil nutrients

The long-term use of chemical fertilizers to maintain agricultural production has had various harmful effects on farmland and has greatly impacted agriculture's sustainable expansion. Graphene, a unique and effective nanomaterial, is used in plant-soil applications to improve plant nutrient uptake, reduce chemical fertilizer pollution by relieving inadequate soil nutrient conditions and enhance soil absorption of nutrient components. We investigated the effects of graphene amendment on nutrient content, maize growth, and soil physicochemical parameters. In each treatment, 5 graphene concentration gradients (0, 25, 50, 100, and 150 g kg^-1) were applied in 2 different types (single-layer and few-layers, SL and FL). Soil aggregates, soil accessible nutrients, soil enzyme activity, plant nutrients, plant height, stem diameter, dry weight, and fresh weight were all measured throughout the maize growth to the V3 stage. Compared to the control (0 g kg^-1), we found that graphene increased the percentage of large agglomerates (0.25-10 mm) in the soil and significantly increased the geometric mean diameter (GMD) and mean weight diameter (MWD) values of > 0.25 mm water-stable agglomerates as the increase of concentration. Soil available nutrient content (AN, AP, and AK) increased, peaking at 150 g kg^-1. Graphene boosted nutrient absorption by maize plants, and aboveground total nitrogen (TN), total phosphorus (TP), and total potassium (TK) contents rose with the increasing application, which raised aboveground fresh weight, dry weight, plant height, and stalk thickness. The findings above confirmed our prediction that adding graphene to the soil may improve maize plant biomass by enhancing soil fertility and improving the soil environment. Given the higher manufacturing cost of single-layer graphene and the greater effect of few-layer graphene on soil and maize plants at the same concentration, single-layer graphene and few-layer graphene at a concentration of 50 g kg^-1 were the optimal application rates.

Comparative Genomics and Functional Studies of Putative m6A Methyltransferase (METTL) Genes in Cotton

N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m6A RNA methyltransferases in cotton. Here, a systematic analysis of the m6A methyltransferase (METTL) gene family was performed on twelve cotton species, resulting in six METTLs identified in five allotetraploid cottons, respectively, and three to four METTLs in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that METTL genes from cottons, Arabidopsis thaliana, and Homo sapiens could be classified into three clades (METTL3, METTL14, and METTL-like clades). Cis-element analysis predicated the possible functions of METTL genes in G. hirsutum. RNA-seq data revealed that GhMETTL14 (GH_A07G0817/GH_D07G0819) and GhMETTL3 (GH_A12G2586/GH_D12G2605) had high expressions in root, stem, leaf, torus, petal, stamen, pistil, and calycle tissues. GhMETTL14 also had the highest expression in 20 and 25 dpa fiber cells, implying a potential role at the cell wall thickening stage. Suppressing GhMETTL3 and GhMETTL14 by VIGS caused growth arrest and even death in G. hirsutum, along with decreased m6A abundance from the leaf tissues of VIGS plants. Overexpression of GhMETTL3 and GhMETTL14 produced distinct differentially expressed genes (DEGs) in A. thaliana, indicating their possible divergent functions after gene duplication. Overall, GhMETTLs play indispensable but divergent roles during the growth of cotton plants, which provides the basis for the systematic investigation of m6A in subsequent studies to improve the agronomic traits in cotton.

Effects of Graphene Oxide on Plant Growth: A Review

Several reports of graphene oxide (GO) promoting plant growth have sparked interest in its potential applications in agroforestry. However, there are still some toxicity studies that have raised concerns about the biosafety of GO. These reports show conflicting results from different perspectives, such as plant physiology, biochemistry, cytology, and molecular biology, regarding the beneficial and detrimental effects of GO on plant growth. Seemingly inconsistent studies make it difficult to effectively apply GO in agroforestry. Therefore, it is crucial to review and analyze the current literature on the impacts of GO on plant growth and its physiological parameters. Here, the biological effects of GO on plant growth are summarized. It is proposed that an appropriate concentration of GO may be conducive to its positive effects, and the particle size of GO should be considered when GO is applied in agricultural applications. This review provides a comprehensive understanding of the effects of GO on plant growth to facilitate its safe and effective use.

De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues

The sequenced data availability opened new horizons related to buffalo genetic control of economic traits and genomic diversity. The visceral organs (brain, liver, etc.) significantly involved in energy metabolism, docility, or social interactions. We performed swamp buffalo transcriptomic profiling of 24 different tissues (brain and non-brain) to identify novel transcripts and analyzed the differentially expressed genes (DEGs) of brain vs. non-brain tissues with their functional annotation. We obtained 178.57 Gb clean transcriptomic data with GC contents 52.77%, reference genome alignment 95.36%, exonic coverage 88.49%. Totally, 26363 mRNAs transcripts including 5574 novel genes were obtained. Further, 7194 transcripts were detected as DEGs by comparing brain vs. non-brain tissues group, of which 3,999 were upregulated and 3,195 downregulated. These DEGs were functionally associated with cellular metabolic activities, signal transduction, cytoprotection, and structural and binding activities. The related functional pathways included cancer pathway, PI3k-Akt signaling, axon guidance, JAK-STAT signaling, basic cellular metabolism, thermogenesis, and oxidative phosphorylation. Our study provides an in-depth understanding of swamp buffalo transcriptomic data including DEGs potentially involved in basic cellular activities and development that helped to maintain their working capacity and social interaction with humans, and also, helpful to disclose the genetic architecture of different phenotypic traits and their gene expression regulation.

Graphene-Delivered Insecticides against Cotton Bollworm

Nanopesticides can facilitate controlled release kinetics and efficiently enhance the permeability of active ingredients to reduce the dosage and loss of pesticides. To clarify the synergistic mechanism of graphene-insecticide nanocarriers against cotton bollworm, treatment groups, namely, control, graphene (G), insecticide (lambda-cyhalothrin (Cyh) and cyfluthrin (Cyf)), and graphene-delivered insecticide groups were used to treat the third-instar larvae of cotton bollworm. The variations in phenotypes, namely, the body length, body weight, and mortality of the cotton bollworm, were analyzed. The results show that graphene enhances the insecticidal activity of lambda-cyhalothrin and cyfluthrin against cotton bollworm. The two graphene-delivered insecticides with optimal compositions (3:1) had the strongest inhibitory effects and the highest mortality rates, with the fatality rates for the 3/1 Cyh/G and Cyf/G mixture compositions being 62.91% and 38.89%, respectively. In addition, the 100 μg/mL Cyh/G mixture had the greatest inhibitory effect on cotton bollworm, and it decreased the body length by 1.40 mm, decreased the weight by 1.88 mg, and had a mortality rate of up to 61.85%. The 100 and 150 μg/mL Cyh/G mixtures achieved the same mortality rate as that of lambda-cyhalothrin, thus reducing the use of the insecticide by one-quarter. The graphene-delivered insecticides could effectively destroy the epicuticle spine cells of the cotton bollworm by increasing the permeability and, thus, the toxicity of the insecticides.

Advances in Biologically Applicable Graphene-Based 2D Nanomaterials

Climate change and increasing contamination of the environment, due to anthropogenic activities, are accompanied with a growing negative impact on human life. Nowadays, humanity is threatened by the increasing incidence of difficult-to-treat cancer and various infectious diseases caused by resistant pathogens, but, on the other hand, ensuring sufficient safe food for balanced human nutrition is threatened by a growing infestation of agriculturally important plants, by various pathogens or by the deteriorating condition of agricultural land. One way to deal with all these undesirable facts is to try to develop technologies and sophisticated materials that could help overcome these negative effects/gloomy prospects. One possibility is to try to use nanotechnology and, within this broad field, to focus also on the study of two-dimensional carbon-based nanomaterials, which have excellent prospects to be used in various economic sectors. In this brief up-to-date overview, attention is paid to recent applications of graphene-based nanomaterials, i.e., graphene, graphene quantum dots, graphene oxide, graphene oxide quantum dots, and reduced graphene oxide. These materials and their various modifications and combinations with other compounds are discussed, regarding their biomedical and agro-ecological applications, i.e., as materials investigated for their antineoplastic and anti-invasive effects, for their effects against various plant pathogens, and as carriers of bioactive agents (drugs, pesticides, fertilizers) as well as materials suitable to be used in theranostics. The negative effects of graphene-based nanomaterials on living organisms, including their mode of action, are analyzed as well.

Effect of the green synthesized rGO and Mg/rGO nanocomposites on the phytochemical assay, toxicity, and metabolism of Mentha longifolia in vitro cultures

Reduced graphene oxide (rGO) and Mg/rGO nanocomposites (NCs) were prepared by an eco-friendly technique using Rosa canina fruit extract. Physicochemical properties and cytotoxicity to Mentha longifolia in vitro cultures of these nanomaterials were examined by using XRD, FESEM, EDX, FT-IR, DLS/zeta potential, UV-Visible, and GC-MS techniques. The characterization techniques confirmed the synthesis of rGO and Mg/rGO NCs with particle sizes less than 20 nm (based on FESEM). In accordance to the biological measurements, rGO showed in vitro cytotoxicity to M. longifolia shoot cultures. Mg/rGO NCs showed no significant difference in the growth parameters except for a decrease in the shoot number at the concentrations of 50 and 150 mg/L and a decrease in the length of the tallest root at the concentrations of 100 and 150 mg/L, however efficiently improved the photosynthetic pigment contents. The phytochemical assay depicted that the total content of volatile compounds was increased in the treated cultures with 25, 50, and 100 mg/L of rGO and Mg/rGO NCs in comparison to the control. Generally, the more oxygenated and hydrocarbon sesquiterpenes were observed in the cultures treated with 25 and 100 mg/L of rGO and 25 and 50 mg/L of Mg/rGO NCs.

The Effects of Graphene-Family Nanomaterials on Plant Growth: A Review

Numerous reports of graphene-family nanomaterials (GFNs) promoting plant growth have opened up a wide range of promising potential applications in agroforestry. However, several toxicity studies have raised growing concerns about the biosafety of GFNs. Although these studies have provided clues about the role of GFNs from different perspectives (such as plant physiology, biochemistry, cytology, and molecular biology), the mechanisms by which GFNs affect plant growth remain poorly understood. In particular, a systematic collection of data regarding differentially expressed genes in response to GFN treatment has not been conducted. We summarize here the fate and biological effects of GFNs in plants. We propose that soil environments may be conducive to the positive effects of GFNs but may be detrimental to the absorption of GFNs. Alterations in plant physiology, biochemistry, cytological structure, and gene expression in response to GFN treatment are discussed. Coincidentally, many changes from the morphological to biochemical scales, which are caused by GFNs treatment, such as affecting root growth, disrupting cell membrane structure, and altering antioxidant systems and hormone concentrations, can all be mapped to gene expression level. This review provides a comprehensive understanding of the effects of GFNs on plant growth to promote their safe and efficient use.

Integrating transcriptome and physiological analyses to elucidate the molecular responses of buckwheat to graphene oxide

With the increasing application of nanomaterials, evaluation of the phytotoxicity of nanoparticles has attracted considerable interest. Buckwheat is an economically pseudocereal crop, which is a potential model for investigating the response of plants to hazardous materials. In this study, the response of buckwheat to graphene oxide (GO) was investigated by integrating physiological and transcriptome analysis. GO can penetrate into buckwheat root and stem, and high concentrations of GO inhibited seedlings growth. High concentration of GO improved ROS production and regulated the activities and gene expression of oxidative enzymes, which implying GO may affect plant growth via regulating ROS detoxification. Root and stem exhibit distinct transcriptomic responses to GO, and the GO-responsive genes in stem are more enriched in cell cycle and epigenetic regulation. GO inhibited plant hormone biosynthesis and signaling by analyzing the expression data. Additionally, 97 small secreted peptides (SSPs) encoding genes were found to be involved in GO response. The gene expression of 111 transcription factor (TFs) and 43 receptor-like protein kinases (RLKs) were regulated by GO, and their expression showed high correlation with SSPs. Finally, the TFs-SSPs-RLKs signaling networks in regulating GO response were proposed. This study provides insights into the molecular responses of plants to GO.

Effects of graphene on morphology, microstructure and transcriptomic profiling of Pinus tabuliformis Carr. roots

Graphene has shown great potential for improving growth of many plants, but its effect on woody plants remains essentially unstudied. In this work, Pinus tabuliformis Carr. bare-rooted seedlings grown outdoors in pots were irrigated with a graphene solution over a concentration range of 0-50 mg/L for six months. Graphene was found to stimulate root growth, with a maximal effect at 25 mg/L. We then investigated root microstructure and carried out transcript profiling of root materials treated with 0 and 25 mg/L graphene. Graphene treatment resulted in plasma-wall separation and destruction of membrane integrity in root cells. More than 50 thousand of differentially expressed genes (DEGs) were obtained by RNA sequencing, among which 6477 could be annotated using other plant databases. The GO enrichment analysis and KEGG pathway analysis of the annotated DEGs indicated that abiotic stress responses, which resemble salt stress, were induced by graphene treatment in roots, while responses to biotic stimuli were inhibited. Numerous metabolic processes and hormone signal transduction pathways were altered by the treatment. The growth promotion effects of graphene may be mediated by encouraging proline synthesis, and suppression of the expression of the auxin response gene SMALL AUXIN UP-REGULATED RNA 41 (SAUR41), PYL genes which encode ABA receptors, and GSK3 homologs.