Glyphosate effects on the gene expression of the apical bud in soybean (Glycine max)

Transcriptomic analysis of codon usage patterns and gene expression characteristics in leafy spurge

Leafy spurge (Euphorbia esula) is an important herb and potential energy source with medicinal value. Codon usage bias (CUB) is a static feature of genes and genomes that results from adaptation and selection during long-term evolution and facilitates molecular breeding in transgenic plants. Here, we used TransDecoder to identify candidate coding regions from the downloaded leafy spurge transcriptome and generate coding region annotation files based on reference genomes. The whole genome showed A/T bias, especially at terminal positions, and seven high-frequency codons were identified. We compared codon usage frequencies to identify candidate exogenous expression receptor systems for leafy spurge. The identified factors affecting leafy spurge CUB included natural selection and other factors, mutation pressure and base composition, with natural selection and other factors being dominant. The observed CUB was significantly positively correlated with the gene expression levels. Systematic analysis of whole-genome leafy spurge revealed that highly expressed protein-coding genes presented greater CUB than did less expressed protein-coding genes. Furthermore, the highly expressed genes tended to have terminal G/C bases. In summary, we conducted a series of related studies based on the leafy spurge whole-genome sequence and laid a foundation for selecting suitable exogenous expression receptor systems and improving gene expression levels.

Molecular responses reveal that two glutathione S-transferase CsGSTU8s contribute to detoxification of glyphosate in tea plants (Camellia sinensis)

Tea plant (Camellia sinensis) is an important economical crop that frequently suffers from various herbicides, especially glyphosate. However, the molecular responses and regulatory mechanisms of glyphosate stress in tea plants remain poorly understood. Here, we reported a transcriptome dataset and identified large number of differentially expressed genes (DEGs) under glyphosate exposure. Next, two glutathione S-transferase genes (CsGSTU8-1 and CsGSTU8-2) that upregulated significantly were screened as candidate genes. Tissue-specific expression patterns showed that both CsGSTU8-1 and CsGSTU8-2 had extremely high expression levels in the roots and were predominantly localized in the nucleus and plasma membrane based on subcellular localization. Both were significantly upregulated at different time points under various stressors, including drought, cold, salt, pathogen infections, and SA treatments. An enzymatic activity assay showed that CsGSTU8-1 catalyzes the conjugation of glutathione with 2,4-dinitrochlorobenzene (CDNB). Functional analysis in yeast verified that the two genes significantly contributed to the detoxification of glyphosate, and CsGSTU8-1 had a stronger role in detoxification than CsGSTU8-2. Taken together, these findings provide insights into the molecular responses of tea plants to glyphosate and the functions of CsGSTU8s in glyphosate detoxification, which can be used as a promising genetic resource for improving herbicide resistance in tea cultivars.

Review on Pesticide Abiotic Stress over Crop Health and Intervention by Various Biostimulants

Plants are essential for life on earth, and agricultural crops are a primary food source for humans. For the One Health future, crop health is crucial for safe, high-quality agricultural products and the development of future green commodities. However, the overuse of pesticides in modern agriculture raises concerns about their adverse effects on crop resistance and product quality. Recently, biostimulants, including microecological bacteria agents and nanoparticles, have garnered worldwide interest for their ability to sustain plant health and enhance crop resistance. This review analyzed the effects and mechanisms of pesticide stress on crop health. It also investigated the regulation of biostimulants on crop health and the multiomics mechanism, combining research on nanoselenium activating various crop health aspects conducted by the authors' research group. The paper helps readers understand the impact of pesticides on crop health and the positive influence of various biostimulants, especially nanomaterials and small molecules, on crop health.

Unravelling the Phytotoxic Effects of Glyphosate on Sensitive and Resistant Amaranthus palmeri Populations by GC-MS and LC-MS Metabolic Profiling

Glyphosate, the most successful herbicide in history, specifically inhibits the activity of the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), one of the key enzymes in the shikimate pathway. Amaranthus palmeri is a driver weed in agriculture today that has evolved glyphosate-resistance through increased EPSPS gene copy number and other mechanisms. Non-targeted GC-MS and LC-MS metabolomic profiling was conducted to examine the innate physiology and the glyphosate-induced perturbations in one sensitive and one resistant (by EPSPS amplification) population of A. palmeri. In the absence of glyphosate treatment, the metabolic profile of both populations was very similar. The comparison between the effects of sublethal and lethal doses on sensitive and resistant populations suggests that lethality of the herbicide is associated with an amino acid pool imbalance and accumulation of the metabolites of the shikimate pathway upstream from EPSPS. Ferulic acid and its derivatives were accumulated in treated plants of both populations, while quercetin and its derivative contents were only lower in the resistant plants treated with glyphosate.

Alleviation of Herbicide Toxicity in Solanum lycopersicum L.-An Antioxidant Stimulation Approach

Application of the herbicide glyphosate in crops is a common practice among farmers around the world. Tomato is one of the crops that are treated with glyphosate to fight weed growth and loss of crop. However, tomato plants often show phytotoxic effects from glyphosate. In this study, the ability of pongamia oil derived from Pongamia pinnata (known also as Millettia pinnata) tree to alleviate the herbicide glyphosate toxicity effects in tomato (S.lycopersicum L. cv. Micro-tom) plants was tested. Tomato plants were treated with a mixture of a dose of (GLY) glyphosate (10 mg kg−1) and different doses of pongamia oil (PO) foliar spray (5, 10, 50, and 100 mM) and compared with the herbicide or oil control (glyphosate 10 mg kg−1 or pongamia oil PO 50 mM). Some morphological features, non-enzymatic and enzymatic antioxidants, and gene expression were observed. Glyphosate-treated plants sprayed with PO 50 mM (GLY + PO 50) showed increased root biomass (0.28 g-p ≤ 0.001), shoot biomass (1.2 g-p ≤ 0.01), H2O2 (68 nmol/g), and the activities of superoxide dismutase (SOD; 40 mg-p ≤ 0.001), catalase (CAT; 81.21 mg-p ≤ 0.05), ascorbate peroxidase (APX; 80 mg-p ≤ 0.01) and glutathione reductase (GR; 53 min/mg-F4,20 = 15.88, p ≤ 0.05). In contrast, these plants showed reduced contents of Malondialdehyde (MDA; 30 nmol/g-F4,20 = 18.55, p ≤ 0.01), O2 (0.6 Abs/g), Prolne (Pro; 345 µg/g), Glutathine (GSH; 341 nmol/mg-p ≤ 0.001), ascorbate (AsA; 1.8 µmol/gm), ascorbic acid (AA; 1.62 mg-p ≤ 0.05) and dehydroascorbate (DHAR; 0.32 mg p ≤ 0.05). The gene expression analysis was conducted for seven oxidative stress related genes besides the house-keeping gene Actin as a reference. The gene CYP1A1450 showed the highest mRNA expression level (6.8 fold ± 0.4) in GLY-treated tomato plants, whereas GLY-treated plants + PO 50 showed 2.9 fold. The study concluded that foliar spray of 50 mM pongamia oil alleviated the toxic effects of glyphosate on tomato plants in the form of increased root and shoot biomass, SOD, CAT, APX, and GR activity, while reduced MDA, O2, Pro, GSH, AsA, AA, DHAR, and gene CYP1A1450 expression.

Comparing field-based management approaches for invasive Winter Heliotrope (Petasites pyrenaicus, Asteraceae)

Winter Heliotrope (Petasites pyrenaicus, previously P. fragrans), is a persistent, rhizome-forming species found throughout the Mediterranean region and North Africa and is an Invasive Alien Plant (IAP) in the UK and Ireland. P. pyrenaicus excludes native flora by forming a dense, compact canopy that persists for much of the growing season, and is often found growing in rough ground, riparian areas and along communication routes, incurring significant management costs at sites of conservation interest. Our study describes the first field-based assessment of P. pyrenaicus control treatments, testing 12 physical and/or chemical treatments in replicated 1 m2 plots over four years and one chemical treatment over three years. Treatments focused on understanding phenology and resource allocation to exploit rhizome source-sink relationships in P. pyrenaicus. Multiple-stage glyphosate- and picloram-based treatments reduced leaf canopy cover to zero (%) over time, though no treatment completely eradicated P. pyrenaicus. When designing management strategies, effective P. pyrenaicus control may be achieved by a single annual soil and/or foliar application of picloram at 1.34 kg AE ha-1 in spring, or by a single annual foliar application of glyphosate in spring at 2.16 kg AE ha-1. Control is not improved by the addition of other herbicides or physical treatment methods, underlining the importance of these herbicides for perennial invasive plant management. This work confirms the importance of considering plant phenology, resource allocation and rhizome source-sink relationships, to increase treatment efficacy and reduce the environmental impacts associated with the management of P. pyrenaicus and other invasive, rhizome forming species.

The moderate oxidative stress induced by glyphosate is not detected in Amaranthus palmeri plants overexpressing EPSPS

The present study aimed to determine whether glyphosate-induced oxidative stress is directly related to the action mechanism of this herbicide (5-enolpyruvylshikimate-3-phosphate synthase or EPSPS inhibition) and analyse the role of oxidative stress in glyphosate toxicity of the weed Amaranthus palmeri S. Wats. Two kinds of populations were studied using EPSPS amplification: glyphosate-sensitive and glyphosate-resistant (by gene amplification). Plants were grown hydroponically and treated with different glyphosate doses, after which several oxidative stress markers were measured in the leaves. Untreated, sensitive and resistant plants showed similar values for the analysed parameters. Treated glyphosate-sensitive plants showed an increase in shikimate, superoxide and H2O2 contents and dose-dependent lipid peroxidation and antioxidant responses; however, none of these effects were observed in resistant plants, indicating that glyphosate-induced oxidative stress is related to EPSPS inhibition. Oxidative stress is associated with an increase in the activity of peroxidases due to EPSPS inhibition, although the link between both processes remains elusive. The fact that some glyphosate doses were lethal but did not induce major oxidative damage provides evidence that glyphosate toxicity is independent of oxidative stress.

New Methods for Testing/Determining the Environmental Exposure to Glyphosate in Sunflower (Helianthus annuus L.) Plants

Glyphosate is still the subject of much debate, as several studies report its effects on the environment. Sunflower (GK Milia CL) was set up as an experimental plant and treated with glyphosate concentrations of 500 ppm and 1000 ppm in two treatments. Glyphosate was found to be absorbed from the soil into the plant organism through the roots, which was also detectable in the leaf and root. Glyphosate was also significantly detected in the plant 5 weeks after treatment and in plants that did not receive glyphosate treatment directly, so it could be taken up through the soil. Based on the morphological results, treatment with higher concentrations (1000 ppm) of glyphosate increased the dried mass and resulted in shorter, thicker roots. Histological results also showed that basal and transporter tissue distortions were observed in the glyphosate-treated plants compared to the control group. Cells were distorted with increasing concentration, vacuoles formed, and the cell wall was weakened in both the leaf-treated and inter-row-treated groups. In the future, it will be worth exploring alternative agricultural technologies that can reduce the risk of glyphosate while increasing economic outcomes. This may make the use of glyphosate more environmentally conscious.

Proteomic Profile of Glyphosate-Resistant Soybean under Combined Herbicide and Drought Stress Conditions

While some genetically modified (GM) plants have been targeted to confer tolerance to abiotic stressors, transgenes are impacted by abiotic stressors, causing adverse effects on plant physiology and yield. However, routine safety analyses do not assess the response of GM plants under different environmental stress conditions. In the context of climate change, the combination of abiotic stressors is a reality in agroecosystems. Therefore, the aim of this study was to analyze the metabolic cost by assessing the proteomic profiles of GM soybean varieties under glyphosate spraying and water deficit conditions compared to their non-transgenic conventional counterparts. We found evidence of cumulative adverse effects that resulted in the reduction of enzymes involved in carbohydrate metabolism, along with the expression of amino acids and nitrogen metabolic enzymes. Ribosomal metabolism was significantly enriched, particularly the protein families associated with ribosomal complexes L5 and L18. The interaction network map showed that the affected module representing the ribosome pathway interacts strongly with other important proteins, such as the chloro-plastic gamma ATP synthase subunit. Combined, these findings provide clear evidence for increasing the metabolic costs of GM soybean plants in response to the accumulation of stress factors. First, alterations in the ribosome pathway indicate that the GM plant itself carries a metabolic burden associated with the biosynthesis of proteins as effects of genetic transformation. GM plants also showed an imbalance in energy demand and production under controlled conditions, which was increased under drought conditions. Identifying the consequences of altered metabolism related to the interaction between plant transgene stress responses allows us to understand the possible effects on the ecology and evolution of plants in the medium and long term and the potential interactions with other organisms when these organisms are released in the environment.

Transcriptome analysis reveals differing response and tolerance mechanism of EPSPS and GAT genes among transgenic soybeans

BACKGROUND

Glyphosate is a broad-spectrum, non-selective systemic herbicide. Introduction of glyphosate tolerance genes such as EPSPS or detoxification genes such as GAT can confer glyphosate tolerance on plants. Our previous study revealed that co-expression of EPSPS and GAT genes conferred higher glyphosate tolerance without "yellow flashing". However, the plant response to glyphosate at the transcriptional level was not investigated.

METHODS AND RESULTS

To investigate the glyphosate tolerance mechanism, RNA-seq was conducted using four soybean genotypes, including two non-transgenic (NT) soybeans, ZH10 and MD12, and two GM soybeans, HJ698 and ZH10-6. Differentially expressed genes (DEGs) were identified in these soybeans before and after glyphosate treatment. Similar response to glyphosate in the two NT soybeans and the different effects of glyphosate on the two GM soybeans were identified. As treatment time was prolonged, the expression level of some DEGs involved in shikimate biosynthetic pathway and herbicide targeted cross-pathways was increased or declined continuously in NT soybeans, and altered slightly in HJ698. However, the expression level of some DEGs was altered in ZH10-6 at 12 hpt, while similar expression level of some DEGs involved in shikimate biosynthetic pathway and herbicide targeted cross-pathways was observed in ZH10-6 at 0 hpt and 72 hpt. These observations likely explain the higher glyphosate tolerance in ZH10-6 than in HJ698 and NT soybeans.

CONCLUSIONS

These results suggested that GAT and EPSPS genes together play a crucial role in response to glyphosate, the GAT gene may work at the early stage of glyphosate exposure, whereas the EPSPS gene may be activated after the uptake of glyphosate by plants. These findings will provide valuable insight for the molecular basis underlying glyphosate tolerance or glyphosate detoxication.

Modulation of Physiological Stress Response of Triticum aestivum L. to Glyphosate by Brassinosteroid Application

The potential of brassinosteroids to modulate the physiological responses of winter wheat (Triticum aestivum L.) to herbicide stress was evaluated. Young winter wheat seedlings were treated with 24-epibrassinolide (EBL) and 24 h later were sprayed with glyphosate. The physiological responses of treated plants were assessed 14 days after herbicide application. Wheat growth was noticeably inhibited by glyphosate. The herbicide application significantly increased the content of the stress markers proline and malondialdehyde (MDA) evidencing oxidative damage. The content of phenolic compounds was decreased in the herbicide-treated plants. Slight activation of superoxide dismutase (SOD) and catalase (CAT) and considerable increase of glutathione reductase (GR) and guaiacol peroxidase (POX) activities were found. Increased POX and glutathione S-transferase (GST) activities were anticipated to be involved in herbicide detoxification. Conjugation with glutathione in herbicide-treated plants could explain the reduction of thiols suggesting unbalanced redox state. EBL application did not alter the plant growth but a moderate activation of antioxidant defense (POX, GR, and CAT activities and phenolic levels) and detoxifying enzyme GST was observed. The hormonal priming provoked a slight decrease in MDA and proline levels. The results demonstrate that EBL-pretreatment partly restored shoot growth and has a potential to mitigate the oxidative damages in glyphosate-treated plants through activation of the enzymatic antioxidant defense and increase of the phenolic compounds.

Glyphosate-Modulated Biosynthesis Driving Plant Defense and Species Interactions

Glyphosate has become the best-selling herbicide used in agriculture, horticulture, silviculture, and urban environments. It disrupts the shikimate metabolic pathway and thereby blocks the production of aromatic amino acids, which are the basis for several plant metabolites. Glyphosate residues are reported in soils from diverse environments, but the effects on plant physiology and consequences for species interactions are largely unknown. Here, we emphasize the complexity of these physiological processes, and argue that glyphosate residues modulate biosynthetic pathways, individually or interactively, which may affect interactions between plants and heterotrophic organisms. In this way, glyphosate residues can substantially interfere with plant resistance and the attraction of beneficial insects, both of which are essential elements in integrated pest management and healthy ecosystems.

Alterations in the 5' untranslated region of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene influence EPSPS overexpression in glyphosate-resistant Eleusine indica

BACKGROUND

The herbicide glyphosate inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Overexpression of the EPSPS gene is one of the molecular mechanisms conferring glyphosate resistance in weeds, but the transcriptional regulation of this gene is poorly understood. The EPSPS gene was found to be significantly up-regulated following glyphosate treatment in a glyphosate-resistant Eleusine indica population from southern China. To further investigate the regulation of EPSPS overexpression, the promoter of the EPSPS gene from this E. indica population was cloned and analyzed.

RESULTS

Two upstream regulatory sequences, Epro-S (862 bp) and Epro-R (877 bp), of EPSPS were obtained from glyphosate-susceptible (S) and -resistant (R) E. indica plants, respectively, by high-efficiency thermal asymmetric interlaced polymerase chain reaction (HiTAIL-PCR). The Epro-S and Epro-R sequences were 99% homologous, except for two insertions (3 and12 bp) in the R sequence. The 12-base insertion in the Epro-R sequence was located in the 5' untranslated region (UTR) pyrimidine nucleotide-rich (Py-rich) stretch element. Promoter activity tests showed that the 12-base insertion resulted in significant enhancement of Epro-R promoter activity, whereas the 3-base insertion had little effect on Epro-R promoter activity.

CONCLUSION

Alterations in the 5' UTR Py-rich stretch element of EPSPS are responsible for glyphosate-induced EPSPS overexpression. Thus, EPSPS transcriptional regulation confers glyphosate resistance in this E. indica population. © 2018 Society of Chemical Industry.

Herbicide Toxicity to Soybean-Rhizobium Symbiosis as Affected by Soil pH

The current study examined whether soil pH could influence the toxicity of herbicides to soybean-rhizobium symbiosis. This can be useful for farmers to minimize the toxicity of them to crop-rhizobium symbiosis via applying their reduced doses. The toxicity of bentazon, metribuzin, and trifluralin to soybean-rhizobium symbiosis was investigated in pH 6.4, 7.2, and 8 soils. Seed inoculation decreased shoot:root (S:R) ratio but increased height, shoot dry weight (SDW), root dry weight (RDW), shoot nitrogen content (SNC), root nitrogen content (RNC), and nitrogen fixation effectiveness (NFE) in the pH 7.2 soil without herbicide application. All herbicides decreased NFE in all soil pH regimes except metribuzin in the pH 6.4 soil. Unlike trifluralin, the toxicity of bentazon and metribuzin to soybean-rhizobium symbiosis was influenced by the soil pH. It can be concluded that soil acidification and alkalization, which can rapidly occur in agroecosystems, can decrease and increase the toxicity of bentazon and metribuzin to soybean-rhizobium symbiosis, respectively.

Optimising physiochemical control of invasive Japanese knotweed

Japanese knotweed, Fallopia japonica var. japonica, causes significant disruption to natural and managed habitats, and provides a model for the control of invasive rhizome-forming species. The socioeconomic impacts of the management of, or failure to manage, Japanese knotweed are enormous, annually costing hundreds of millions of pounds sterling (GBP£) in the UK alone. Our study describes the most extensive field-based assessment of F. japonica control treatments undertaken, testing the largest number of physical and/or chemical control treatments (19 in total) in replicated 225 m2 plots over 3 years. Treatments focused on phenology, resource allocation and rhizome source–sink relationships to reduce the ecological impacts of controlling F. japonica. While no treatment completely eradicated F. japonica, a multiple-stage glyphosate-based treatment approach provided greatest control. Increasing herbicide dose did not improve knotweed control, but treatments that maximised glyphosate coverage, e.g., spraying versus stem injection, and exploited phenological changes in rhizome source–sink relationships caused the greatest reduction of basal cover and stem density after 3 years. When designing management strategies, effective control of F. japonica may be achieved by biannual (summer and autumn) foliar glyphosate applications at 2.16 kg AE ha−1, or by annual application of glyphosate in autumn using stem injection at 65.00 kg AE ha−1 or foliar spray at 3.60 kg AE ha−1. Addition of other herbicides or physical treatment methods does not improve control. This work demonstrates that considering phenology, resource allocation and rhizome source–sink relationships is critical for the control of invasive, rhizome forming species.

Responses of Hydrilla verticillata (L.f.) Royle and Vallisneria natans (Lour.) Hara to glyphosate exposure

Glyphosate is a broad-spectrum herbicide that is frequently detected in water bodies and is harmful to aquatic systems. We conducted an experiment to explore the ecological sensitivity of Hydrilla verticillata (L.f.) Royle and Vallisneria natans (Lour.) Hara to glyphosate. Our research focused on the physiological responses of H. verticillata and V. natans after exposure to various concentrations of glyphosate (0, 1, 10, 20, 30, 40, 50 and 80 mg/L) in hydroponic culture after one day (1D) and seven days (7D). The results show that after 1D, the soluble protein content of H. verticillata was significantly stimulated under low herbicide concentrations. Other indices for H. verticillata and V. natans had no remarkable changes at 1D. After 7D of treatment, the soluble protein content of H. verticillata showed no significant differences, while the malondialdehyde (MDA), pigment contents and catalase (CAT) activity significantly increased at low glyphosate concentrations. Guaiacol peroxidase (POD) activity in H. verticillata significantly increased with increasing herbicide concentrations. The chlorophyll a/b ratio of H. verticillata sharply decreased above 10 mg/L. For V. natans, soluble protein, chlorophyll a, and carotenoid content; and CAT activity declined significantly after glyphosate application, while other indicators showed no significant changes. Our results indicate that glyphosate concentrations from 0 to 80 mg/L can induce oxidative stress in H. verticillate and may impede metabolism processes for protein and pigments without causing oxidative stress in V. natans. Taken together, our results suggest that the sensitivity of H. verticillata to glyphosate exposure is higher than that of V. natans.

Alteration of plant physiology by glyphosate and its by-product aminomethylphosphonic acid: an overview

It is generally claimed that glyphosate kills undesired plants by affecting the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme, disturbing the shikimate pathway. However, the mechanisms leading to plant death may also be related to secondary or indirect effects of glyphosate on plant physiology. Moreover, some plants can metabolize glyphosate to aminomethylphosphonic acid (AMPA) or be exposed to AMPA from different environmental matrices. AMPA is a recognized phytotoxin, and its co-occurrence with glyphosate could modify the effects of glyphosate on plant physiology. The present review provides an overall picture of alterations of plant physiology caused by environmental exposure to glyphosate and its metabolite AMPA, and summarizes their effects on several physiological processes. It particularly focuses on photosynthesis, from photochemical events to C assimilation and translocation, as well as oxidative stress. The effects of glyphosate and AMPA on several plant physiological processes have been linked, with the aim of better understanding their phytotoxicity and glyphosate herbicidal effects.