Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies

Simulated herbicide mixtures delay both specialist monogenic and generalist polygenic resistance evolution in weeds

BACKGROUND

Evolution of herbicide-resistant weed populations is a major challenge to world food production. Using different herbicides in rotation and/or using different herbicides together as mixtures are strategies that may delay the selection of resistance. This study used simulation modelling to investigate whether mixtures and rotations can delay the selection of both generalist polygenic and specialist monogenic herbicide resistance, and whether these strategies are more likely to lead to the selection of generalist resistance in weed types with varying biological characteristics.

RESULTS

Our simulations suggest that well-designed effective herbicide mixtures should delay evolution of both polygenic and monogenic resistance better than rotations and single herbicides across all weed types. Both mixture and rotation strategies increased the likelihood of polygenic resistance compared to single-herbicide use, and the likelihood of polygenic resistance increased as the fecundity and competitiveness of the weed increased. Whether monogenic or polygenic resistance occurred in each case depended most on the relative initial allele frequencies. We did not find that herbicide mixtures were more likely than rotations to lead to the selection of generalist polygenic resistance. The simulated efficacy of mixtures over rotations decreased if components were used at reduced rates or when individual components had already been used solo.

CONCLUSION

Herbicide rotations and particularly well-designed mixtures should delay evolution of both polygenic and monogenic resistance, especially if used as part of an effective integrated weed management programme. However, herbicide mixtures and rotations may also increase the risk that resistance will be generalist polygenic rather than specialist monogenic. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Phenotypic Characteristics and Occurrence Basis of Leaf Necrotic Spots in Response of Weedy Rice to Imazethapyr

Weedy rice is the most challenging weed species to remove in rice production. We found a novel phenotype of seedling leaves which rapidly generates necrotic spots in response to imidazolinone herbicides in weedy rice, but its influencing factors and formation basis are still unknown. In this study, we used the leaf necrotic spot-producing type of weedy rice as the material. First, leaf necrotic spots were defined as physiological and vacuole-mediated cell necrosis by microscopic examination. The imazethapyr concentration was positively correlated with the degree of necrotic spots occurring, while the action site was in accordance with necrosis using herbicide stability tests combined with fluorescence parameters. Furthermore, transcriptome analysis revealed significant differences in the gene expression of endoplasmic reticulum stress and the lipid metabolism membrane structure damage pathway during necrosis, as confirmed by transmission electron microscopy. The light-temperature test also showed that high temperature and intense light could promote the appearance of necrotic spots. These experimental results are helpful in clarifying the process and basis of imazethapyr in inducing the rapid generation of necrotic spots in rice leaves and providing new insight into understanding the mechanism of response to imidazolinone herbicides and the control of weedy rice.

Progress in environmental monitoring and mitigation strategies for herbicides and insecticides: A comprehensive review

Herbicides and insecticides are pervasively applied in agricultural sector to increase the yield by controlling or eliminating bug vermin and weeds. Although, resistance development occurs, direct and indirect impact on human health and ecosystem is clearly visible. Normally, herbicides and pesticides are water soluble in nature; accordingly, it is hard to decrease their deadliness and to dis-appear them from the environment. They are profoundly specific, and considered as poisonous to various peoples in agricultural and industrial work places. In order to substantially reduce the harmful impacts, it is crucial to thoroughly examine the detection and mitigation measures for these compounds. The primary objective of this paper is to provide an overview of various herbicide and pesticide detection techniques and associated remedial techniques. A short summary on occurrence and harmful effects of herbicides/insecticides on ecosystem has been included to the study. The conventional and advanced, rapid techniques for the detection of insecticides and herbicides were described in detail. A detailed overview on several mitigation strategies including advanced oxidation, adsorption, electrochemical process, and bioremediation as well as the mechanism behind the strategic approaches to reduce the effects of growing pesticide pollution has been emphasized. Regardless of the detection techniques and mitigation strategies, the recent advances employed, obstacles, and perspectives have been discussed in detail.

Prevalence, spatial structure and evolution of resistance to acetolactate-synthase (ALS) inhibitors and 2,4-D in the major weed Papaver rhoeas (L.) assessed using a massive, country-wide sampling

BACKGROUND

Corn poppy (Papaver rhoeas) is the most damaging broadleaf weed in France. Massively parallel amplicon sequencing was used to investigate the prevalence, mode of evolution and spread of resistance-endowing ALS alleles in 422 populations randomly sampled throughout poppy's range in France. Bioassays were used to detect resistance to the synthetic auxin 2,4-D in 43 of these populations.

RESULTS

A total of 21 100 plants were analysed and 24 mutant ALS alleles carrying an amino-acid substitution involved or potentially involved in resistance were identified. The vast majority (97.6%) of the substitutions occurred at codon Pro197, where all six possible single-nucleotide non-synonymous substitutions plus four double-nucleotide substitutions were identified. Changes observed in the enzymatic properties of the mutant ALS isoforms could not explain the differences in prevalence among the corresponding alleles. Sequence read analysis showed that mutant ALS alleles had multiple, independent evolutionary origins, and could have evolved several times independently within an area of a few kilometres. Finally, 2,4-D resistance was associated with mutant ALS alleles in individual plants in one third of the populations assayed.

CONCLUSION

The intricate geographical mosaic of mutant ALS alleles observed is the likely result of the combination of huge population sizes, multiple independent mutation events and human-mediated spread of resistance. Our work highlights the ability of poppy populations and individual plants to accumulate different ALS alleles and as yet unknown mechanisms conferring resistance to synthetic auxins. This does not bode well for the continued use of chemical herbicides to control poppy. © 2023 Society of Chemical Industry.

Integrating transcriptome and physiological analyses to elucidate the molecular responses of sorghum to fluxofenim and metolachlor herbicide

The extensive use of herbicides has raised concerns about crop damage, necessitating the development of effective herbicide safeners. Fluxofenim has emerged as a promising herbicide safener; however, it's underlying mechanism remains unclear. Here, we screened two inbred lines 407B and HYZ to investigate the detoxication of fluxofenim in mitigating metolachlor damage in sorghum. Metolachlor inhibited seedling growth in both 407B and HYZ, while, fluxofenim could significantly restore the growth of 407B, but not effectively complement the growth of HYZ. Fluxofenim significantly increased the activities of glutathione-S-transferase (GST) to decrease metolachlor residue in 407B, but not in HYZ. This implys that fluxofenim may reduce metolachlor toxicity by regulating its metabolism. Furthermore, metolachlor suppressed AUX-related and JA-related genes expression, while up-regulated the expression of SA-related genes. Fluxofenim also restored the expression of AUX-related and JA-related genes inhibited by metolachlor and further increased expression of SA-related genes. Moreover, we noted a significant increase in the content of trans-zeatin O-glucoside (tZOG) and Gibberellin1 (GA1) after the fluxofenim treatment. In conclusion, fluxofenim may reduce the injury of herbicide by affecting herbicide metabolism and regulating hormone signaling pathway.

First Report on Resistance to HPPD Herbicides Mediated by Nontarget-Site Mechanisms in the Grass Leptochloa chinensis

The emergence of 4-hydroxyphenylpyruvate dioxygenase (HPPD) herbicides as efficacious target-site herbicides has been noteworthy. In recent years, only four species of broadleaf weeds have developed resistance due to the long-term widespread use of HPPD herbicides. This study represents the first reported instance of a grass weed exhibiting resistance to HPPD inhibitors. We identified a new HPPD-resistant Chinese sprangletop [Leptochloa chinensis (L.) Nees] population (R population). At the recommended dose of tripyrasulfone, the inhibition rate of the R population was only half that of the sensitive population (S). The mechanism underlying resistance does not involve target-site resistance triggered by amino acid mutations or depend on disparities within the HPPD INHIBITOR SENSITIVE 1 (HIS1) gene. The impetus for resistance appears to be interlinked with the metabolic activities of cytochrome P450 monooxygenase (P450) and glutathione S-transferase (GST) family genes. Following RNA sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) validation, the study suggests that five P450 genes, CYP71C1, CYP74A2, CYP72A1, CYP84A1, and CYP714C2, alongside a single GST gene GSTF1, may be implicated in the process of metabolic detoxification.

Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus

BACKGROUND

Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are two dioecious and important weed species in the world that can rapidly evolve herbicide-resistance traits. Understanding these two species' dioecious and sex-determination mechanisms could open opportunities for new tools to control them. This study aims to identify the differential expression patterns between males and females in A. tuberculatus and A. palmeri. Multiple analyses, including differential expression, co-expression, and promoter analyses, used RNA-seq data from multiple tissue types to identify putative essential genes for sex determination in both dioecious species.

RESULTS

Genes were identified as potential key players for sex determination in A. palmeri. Genes PPR247, WEX, and ACD6 were differentially expressed between the sexes and located at scaffold 20 within or near the male-specific Y (MSY) region. Multiple genes involved with flower development were co-expressed with these three genes. For A. tuberculatus, no differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were identified as differentially expressed and possible candidate genes.

CONCLUSIONS

This is the first study comparing the global expression profile between males and females in dioecious weedy Amaranthus species. Results narrow down putative essential genes for sex-determination in A. palmeri and A. tuberculatus and also strengthen the hypothesis of two different evolutionary events for dioecy within the genus.

Influence of Season and Habitat on the Essential Oils Composition, Allelopathy, and Antioxidant Activities of Artemisia monosperma Delile

Plants belonging to the Artemisia genus (Asteraceae) are widely distributed worldwide and have many ethnopharmacological, traditional, therapeutic, and phytochemical aspects. Artemisia monosperma is an important aromatic plant due to its traditional and therapeutic uses and phytochemical diversity, including essential oils (EOs). The EO chemical profile of aromatic plants has been reported to be affected by exogenous and endogenous factors. Geographic and seasonal variations are crucial factors shaping the chemical composition of the EO. Herein, the variations of the yields, chemical profiles, and allelopathic and antioxidant activities of A. monosperma EOs collected from three regions in four seasons were assessed. A slight variation in the oil yields was observed among regions and seasons, while the chemical profile, characterized via GC-MS, exhibited significant quantitative and qualitative variation among either regions or seasons. Sesquiterpenes were the main components of all EOs, with significant variation in concentration. In most EO samples, the summer-plant samples had the highest concentration of sesquiterpenes, followed by spring, winter, and autumn. The 7-epi-trans-sesquisabinene hydrate, 6-epi-shyobunol, dehydro-cyclolongifolene oxide, isoshyobunone, diepicedrene-1-oxide, dehydro-aromadendrene, and junipene were the main compounds of all the EO samples. The extracted EOs of the A. monosperma samples showed considerable allelopathic activity against the weed Dactyloctenium aegyptium and the crop Lactuca sativa. A significant variation in allelopathic activity was observed among samples collected during different seasons, while the samples of the autumn and summer seasons had more potential. Also, L. sativa was more affected by the EO compared to D. aegyptium, reflecting that weeds are more resistant to allelochemicals. In this context, the EOs of A. monosperma samples exhibited substantial antioxidant activity with the same pattern of allelopathic activity, whereas the samples of the autumn and summer seasons showed higher antioxidant activity. These biological activities of the EOs could be ascribed to the higher content of oxygenated compounds. The present study revealed that seasons have a substantial effect on EO production as well as composition. In consequence, the biological activities varied with the variation of the chemical profile of the EO. These results show the importance of season/timing for sampling aromatic plants.

Structure-Based Design of 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor as a Potential Herbicide for Cotton Fields

4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is one of the most promising herbicide targets for the development of agricultural chemicals owing to its unique mechanism of action in plants. We previously reported on the co-crystal structure of Arabidopsis thaliana (At) HPPD complexed with methylbenquitrione (MBQ), an inhibitor of HPPD that we previously discovered. Based on this crystal structure, and in an attempt to discover even more effective HPPD-inhibiting herbicides, we designed a family of triketone-quinazoline-2,4-dione derivatives featuring a phenylalkyl group through increasing the interaction between the substituent at the R¹ position and the amino acid residues at the active site entrance of AtHPPD. Among the derivatives, 6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-(1-phenylethyl)quinazoline-2,4(1H,3H)-dione (23) was identified as a promising compound. The co-crystal structure of compound 23 with AtHPPD revealed that hydrophobic interactions with Phe392 and Met335, and effective blocking of the conformational deflection of Gln293, as compared with that of the lead compound MBQ, afforded a molecular basis for structural modification. 3-(1-(3-Fluorophenyl)ethyl)-6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethylquinazoline-2,4(1H,3H)-dione (31) was confirmed to be the best subnanomolar-range AtHPPD inhibitor (IC₅₀ = 39 nM), making it approximately seven times more potent than MBQ. In addition, the greenhouse experiment showed favorable herbicidal potency for compound 23 with a broad spectrum and acceptable crop selectivity against cotton at the dosage of 30-120 g ai/ha. Thus, compound 23 possessed a promising prospect as a novel HPPD-inhibiting herbicide candidate for cotton fields.

The bioherbicidal potential of isolated fungi cultivated in microalgal biomass

This study evaluated the bioherbicidal potential of wild fungi grown on microalgal biomass from the digestate treatment of biogas production. Four fungal isolates were used and the extracts were evaluated for the activity of different enzymes and characterized by gas chromatography coupled with mass spectrometry. The bioherbicidal activity was assessed by application on Cucumis sativus, and the leaf damage was visually estimated. The microorganisms showed potential as agents producing an enzyme pool. The obtained fungal extracts presented different organic compounds, most acids, and when applied to Cucumis sativus, showed high levels of leaf damage (80-100 ± 3.00%, deviation relative to the observed average damage). Therefore, the microbial strains are potential biological control agents of weeds, which, together with the microalgae biomass, offer the appropriate conditions to obtain an enzyme pool of biotechnological relevance and with favorable characteristics to be explored as bioherbicides, addressing aspects within the environmental sustainability.

Herbicide Use in the Era of Farm to Fork: Strengths, Weaknesses, and Future Implications

Climate change mitigation is a major concern of the European Union (EU). In 2019, the EU presented the European Green Deal (EGD), a new environmental strategy that aimed to neutralize climate change by 2050. Within its policy areas, the EGD included the Farm to Fork (F2F) Strategy that aims to reduce pesticide use by 50%, by 2030. This reduction was proposed due to the supposed negative effects of pesticides on the environment and its biota. Among the different pesticide groups (herbicides, fungicides, insecticides, etc.) though, herbicides are perhaps the hardest to reduce. This review aimed to shed light to any factors that might hinder the reduction of herbicide use; thus, the implementation of the Farm to Fork Strategy underlines some of its weaknesses and highlights key points of a viable herbicide reduction-related policy framework. The literature suggests that integrated weed management (IWM) consists perhaps the most suitable approach for the reduction of herbicides in the EU. Even though it is too soon to conclusively assess F2F, its success is not impossible.

Determination and Quantification of Phytochemicals from the Leaf Extract of Parthenium hysterophorus L. and Their Physio-Biochemical Responses to Several Crop and Weed Species

This current investigation was undertaken both in laboratory and glasshouse for documentation and quantification of phytochemicals from different parts of the parthenium (Parthenium hysterophorus L.) plant through LC-MS and HPLC to study their effect on two crops namely, Bambara groundnut (Vigna subterranean L.) and maize (Zea mays L.), and six different types of weed e.g., Digitaria sanguinalis, Eleusine indica, Ageratum conyzoides, Cyperus iria, Euphorbia hirta, and Cyperus difformis. The parthenium methanolic leaf extracts at 25, 50, 75, and 100 g L^-1 were sprayed in the test crops and weeds to assess their physiological and biochemical reactions after 6, 24, 48, and 72 h of spraying these compounds (HAS). The LC-MS analysis confirmed seven types of phytochemicals (caffeic acid, ferulic acid, vanillic acid, parthenin, chlorogenic acid, quinic acid, and p-anisic acid) in the parthenium leaf extract that were responsible for the inhibition of tested crops and weeds. From the HPLC analysis, higher amounts in leaf methanol extracts (40,752.52 ppm) than those of the stem (2664.09 ppm) and flower extracts (30,454.33 ppm) were recorded. Parthenium leaf extract at 100 g L^-1 had observed higher phytotoxicity on all weed species except C. difformis. However, all crops were found safe under this dose of extraction. Although both crops were also affected to some extent, they could recover from the stress after a few days. The photosynthetic rate, transpiration rate, stomatal conductance, carotenoid and chlorophyll content were decreased due to the application of parthenium leaf extract. However, when parthenium leaf extract was applied at 100 g L^-1 for 72 h, the malondialdehyde (MDA) and proline content were increased in all weeds. Enzymatic antioxidant activity (e.g., superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) contents) were also elevated as a result of the sprayed parthenium leaf extract. The negative impact of physiological and biochemical responses as a consequence of the parthenium leaf extract led the weed species to be stressed and finally killed. The current findings show the feasibility of developing bioherbicide from the methanolic extract of parthenium leaf for controlling weeds, which will be cost-effective, sustainable, and environment friendly for crop production during the future changing climate.

Early detection, herbicide resistance screening, and integrated management of invasive plant species: a review

Invasive plant species (IPS) are often considered weeds that cause high yield losses in crops, negatively affect the environment, and disrupt certain ecosystem services. The negative impact of IPS on biodiversity is increasing and disturbing native vegetation. The management of plant invasions can be divided in two phases (before and after invasion). Prior to introduction it is crucial to develop the knowledge base (biology, ecology, distribution, impact, management) on IPS, prevention measures and risk assessment. After introduction if eradication fails, the monitoring and the integrated management of IPS are imperative to prevent the naturalization and further dispersal. This review uses two major invasive weed species (Amaranthus palmeri S. Wats. and Solanum elaeagnifolium Cav.) as case studies to propose a framework for early detection, rapid herbicide resistance screening, and integrated management. The holistic framework that is presented exploits recent: (i) novel detection tools, (ii) rapid tests and assays for herbicide resistance, and (iii) biology, ecology, distribution traits, and management tools for the IPS. Farmers, advisors, researchers, and policymakers need briefing on IPS growth dynamics, adaptability rates, and response to conventional and novel treatments to prevent new invasions, eradicate isolated stands, and mitigate the impact of invasive weed species in the long term. © 2022 Society of Chemical Industry.

Directed Evolution of Phi Class Glutathione Transferases Involved in Multiple-Herbicide Resistance of Grass Weeds and Crops

The extensive application of herbicides in crop cultivation has indisputably led to the emergence of weed populations characterized by multiple herbicide resistance (MHR). This phenomenon is associated with the enhanced metabolism and detoxifying ability of endogenous enzymes, such as phi class glutathione transferases (GSTFs). In the present work, a library of mutant GSTFs was created by in vitro directed evolution via DNA shuffling. Selected gstf genes from the weeds Alopecurus myosuroides and Lolium rigidum, and the cereal crops Triticum durum and Hordeum vulgare were recombined to forge a library of novel chimeric GSTFs. The library was activity screened and the best-performing enzyme variants were purified and characterized. The work allowed the identification of enzyme variants that exhibit an eight-fold improvement in their catalytic efficiency, higher thermal stability (8.3 °C) and three-times higher inhibition sensitivity towards the herbicide butachlor. The crystal structures of the best-performing enzyme variants were determined by X-ray crystallography. Structural analysis allowed the identification of specific structural elements that are responsible for k_cat regulation, thermal stability and inhibition potency. These improved novel enzymes hold the potential for utilization in biocatalysis and green biotechnology applications. The results of the present work contribute significantly to our knowledge of the structure and function of phi class plant GSTs and shed light on their involvement in the mechanisms of MHR.

Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots

Herbicides are key weed-control tools, but their repeated use across large areas has favored the evolution of herbicide resistance. Although target-site has been the most prevalent and studied type of resistance, non-target-site resistance (NTSR) is increasing. However, the genetic factors involved in NTSR are widely unknown. In this study, four gene groups encoding putative NTSR enzymes, namely, cytochrome-P450, glutathione-S-transferase (GST), uridine 5'-diphospho-glucuronosyltransferase (UDPGT), and nitronate monooxygenase (NMO) were analyzed. The monocot and dicot gene sequences were downloaded from publicly available databases. Phylogenetic trees revealed that most of the CYP450 resistance-related sequences belong to CYP81 (5), and in GST, most of the resistance sequences belonged to GSTU18 (9) and GSTF6 (8) groups. In addition, the study of upstream promoter sequences of these NTSR genes revealed stress-related cis-regulatory motifs, as well as eight transcription factor binding sites (TFBS) were identified. The discovered TFBS were commonly present in both monocots and dicots, and the identified motifs are known to play key roles in countering abiotic stress. Further, we predicted the 3D structure for the resistant CYP450 and GST protein and identified the substrate recognition site through the homology approach. Our description of putative NTSR enzymes may be used to develop innovative weed control techniques to delay the evolution of NTSR.

Biopriming of Maize Seeds with a Novel Bacterial Strain SH-6 to Enhance Drought Tolerance in South Korea

Maize is the third most common cereal crop worldwide, after rice and wheat, and plays a vital role in preventing global hunger crises. Approximately 50% of global crop yields are reduced by drought stress. Bacteria as biostimulants for biopriming can improve yield and enhance sustainable food production. Further, seed biopriming stimulates plant defense mechanisms. In this study, we isolated bacteria from the rhizosphere of Artemisia plants from Pohang beach, Daegu, South Korea. Twenty-three isolates were isolated and screened for growth promoting potential. Among them, bacterial isolate SH-6 was selected based on maximum induced tolerance to polyethylene glycol-simulated drought. SH-6 showed ABA concentration = 1.06 ± 0.04 ng/mL, phosphate solubilizing index = 3.7, and sucrose concentration = 0.51 ± 0.13 mg/mL. The novel isolate SH-6 markedly enhanced maize seedling tolerance to oxidative stress owing to the presence of superoxide dismutase, catalase, and ascorbate peroxidase activities in the culture media. Additionally, we quantified and standardized the biopriming effect of SH-6 on maize seeds. SH-6 significantly increased maize seedling drought tolerance by up to 20%, resulting in 80% germination potential. We concluded that the novel bacterium isolate SH-6 (gene accession number (OM757882) is a biostimulant that can improve germination performance under drought stress.

Agronomic and Environmental Determinants of Direct Seeded Rice in South Asia

Rice (Oryza sativa L.) is the staple food of more than 50% of the world's population. Manual puddled transplanted rice (PTR) system is still the predominant method of rice establishment. However, due to declining water tables, increasing water scarcity, water, labor- and energy-intensive nature of PTR, high labor wages, adverse effects of puddling on soil health and succeeding crops, and high methane emissions, this production system is becoming less profitable. These factors trigger the need for an alternative crop establishment method. The direct-seeded rice (DSR) technique is gaining popularity because of its low input demand compared to PTR. It is done by sowing pre-germinated seeds in puddled soil (wet-DSR), standing water (water seeding), or dry seeding on a prepared seedbed (dry-DSR). DSR requires less water and labor (12-35%), reduces methane emissions (10-90%), improves soil physical properties, involves less drudgery and production cost (US$9-125 per hectare), and gives comparable yields. Upgraded short-duration and high-yielding varieties and efficient nutrient, weed, and resource management techniques encouraged the farmers to switch to DSR culture. However, several constraints are associated with this shift: more weeds, the emergence of weedy rice, herbicide resistance, nitrous oxide emissions, nutrient disorders, primarily N and micro-nutrients, and an increase in soil-borne pathogens lodging etc. These issues can be overcome if proper weed, water, and fertilizer management strategies are adopted. Techniques like stale bed technique, mulching, crop rotation, Sesbania co-culture, seed priming, pre-emergence and post-emergence spray, and a systematic weed monitoring program will help reduce weeds. Chemical to biotechnological methods like herbicide-resistant rice varieties and more competitive allelopathic varieties will be required for sustainable rice production. In addition, strategies like nitrification inhibitors and deep urea placement can be used to reduce N₂O emissions. Developing site and soil-specific integrated packages will help in the broader adoption of DSR and reduce the environmental footprint of PTR. The present paper aims to identify the gaps and develop the best-bet agronomic practices and develop an integrated package of technologies for DSR, keeping in mind the advantages and constraints associated with DSR, and suggest some prospects. Eco-friendly, cost-effective DSR package offers sustainable rice production systems with fewer resources and low emissions.

Graphical abstract

History of Herbicide-Resistant Traits in Cotton in the U.S. and the Importance of Integrated Weed Management for Technology Stewardship

This paper reviews the history of herbicide-resistant (HR) traits in U.S. cotton since the beginning, highlighting the shortcomings of each trait over time that has led to the development of their successor and emphasizing the importance of integrated weed management (IWM) going forward to ensure their long-term sustainability. Introduction of glyphosate-resistant cropping systems has allowed for expansion of no-till systems more reliant on herbicides, favored less diverse crop rotations, and heavily relied on a single herbicide mode of action (MOA). With repeated applications of glyphosate over the years, biotypes of glyphosate-resistant (GR) A. palmeri and other weeds became economically damaging pests in cotton production systems throughout the U.S. Moreover, the reported cases of weeds resistant to different MOA across various parts of the United States has increased. The dicamba- (XtendFlex^®) and 2,4-D-resistant (Enlist^®) cotton traits (with stacks of glyphosate and glufosinate resistance) were introduced and have been highly adopted in the U.S. to manage HR weeds. Given the current rate of novel herbicide MOA discovery and increase in new HR weed cases, the future of sustainable weed management relies on an integrated approach that includes non-herbicidal methods with herbicides to ensure long-term success.

Phytotoxicity Optimization of Fungal Metabolites Produced by Solid and Submerged Fermentation and its Ecotoxicological Effects

Research and commercial production of bioherbicides occur to a lesser extent compared to bioinsecticides and biofungicides. In order to contribute to developing new bioherbicides with low environmental impact, this study aimed to increase the phytotoxicity of metabolites of the fungus Mycoleptodiscus indicus UFSM 54 by optimizing solid and submerged fermentation and evaluate the ecotoxicological effects on earthworms (Eisenia andrei). The Plackett-Burman and central composite rotatable designs were used to optimize metabolite phytotoxicity. The variables optimized in the fermentation were temperature, agitation, pH, water volume in the culture medium, glucose concentration, and yeast extract. The fungus was grown on sugarcane bagasse substrate, and its metabolites were applied to detached Cucumis sativus, Conyza sp., and Sorghum bicolor leaves and used in an avoidance test and acute exposure to earthworms. Metabolite phytotoxicity in submerged fermentation was optimized at 35 °C, 50 rpm, and 1.5 g l^-1 of glucose and in solid fermentation at 30-37 °C and in 14-32 ml of water. The metabolites severely damaged germination, initial growth, and leaves of the three plants, and at the doses tested (maximum of 113.92 ml kg^-1), the metabolites of M. indicus UFSM 54 were not toxic to earthworms.

The Impact of Different Weed Management Systems on Weed Flora and Dry Biomass Production of Barley Grown under Various Barley-Based Cropping Systems

Weeds are among the major issues responsible for reduction in yield and profit in any crop production system. Herbicides are the easiest and quickest solution of weeds; however, their frequent use exert negative consequences on environment, human health, and results in the evolution of herbicide-resistant weed species. Due to these reasons, alternative weed management methods that are less harmful to environment and human health are needed. This two-year study evaluated the impact of different weed management options, i.e., false seedbed (FS), allelopathic water extracts (AWE), chemical control (CC), weed-free (WF) weedy-check (WC) on weed spectrum in various barley-based cropping systems, i.e., fallow-barley (FB), maize-barley (MB), cotton-barley (CB), mungbean-barley (M*B), and sorghum-barley (SB). Data relating to density, diversity, and biomass production of weed species prevailing in the studied cropping systems were recorded. Interactive effect of weed management methods and barley-based cropping systems significantly altered weed diversity, and densities of individual, broadleaved, and grassy weeds. A total 13 weed species (ten broadleaved and three grass) were recorded during both years of study. The highest dry biomass, diversity, and density of individual, broadleaved, and grassy weeds were noted in WC treatment, whereas WF treatment resulted in the lowest values of these traits. Chemical control resulted in the highest suppression of weed flora and improved dry biomass production of barley followed by AWE. The SB cropping system with CC or AWE resulted in the least weed flora. The M*B cropping system with CC or AWE produced the highest dry biomass of barley. It is concluded that including sorghum crop in rotation and applying AWE could suppress weeds comparable to herbicides. Similarly, including mungbean in rotation and applying AWE could increase dry biomass production of barley. In conclusion, herbicides can be replaced with an eco-friendly approach, i.e., allelopathy and inclusion of sorghum crop could be helpful in suppressing weed flora.

Identification and Comprehensive Evaluation of Resistant Weeds Using Unmanned Aerial Vehicle-Based Multispectral Imagery

Atrazine is one of the most widely used herbicides in weed management. However, the widespread use of atrazine has concurrently accelerated the evolution of weed resistance mechanisms. Resistant weeds were identified early to contribute to crop protection in precision agriculture before visible symptoms of atrazine application to weeds in actual field environments. New developments in unmanned aerial vehicle (UAV) platforms and sensor technologies promote cost-effective data collection by collecting multi-modal data at very high spatial and spectral resolution. In this study, we obtained multispectral and RGB images using UAVs, increased available information with the help of image fusion technology, and developed a weed spectral resistance index, WSRI = (RE-R)/(RE-B), based on the difference between susceptible and resistant weed biotypes. A deep convolutional neural network (DCNN) was applied to evaluate the potential for identifying resistant weeds in the field. Comparing the WSRI introduced in this study with previously published vegetation indices (VIs) shows that the WSRI is better at classifying susceptible and resistant weed biotypes. Fusing multispectral and RGB images improved the resistance identification accuracy, and the DCNN achieved high field accuracies of 81.1% for barnyardgrass and 92.4% for velvetleaf. Time series and weed density influenced the study of weed resistance, with 4 days after application (4DAA) identified as a watershed timeframe in the study of weed resistance, while different weed densities resulted in changes in classification accuracy. Multispectral and deep learning proved to be effective phenotypic techniques that can thoroughly analyze weed resistance dynamic response and provide valuable methods for high-throughput phenotyping and accurate field management of resistant weeds.

Biotechnological Road Map for Innovative Weed Management

In most agriculture farmlands, weed management is predominantly reliant on integrated weed management (IWM) strategies, such as herbicide application. However, the overuse and misuse of herbicides, coupled with the lack of novel active ingredients, has resulted in the uptrend of herbicide-resistant weeds globally. Moreover, weedy traits that contribute to weed seed bank persistence further exacerbate the challenges in weed management. Despite ongoing efforts in identifying and improving current weed management processes, the pressing need for novel control techniques in agricultural weed management should not be overlooked. The advent of CRISPR/Cas9 gene-editing systems, coupled with the recent advances in "omics" and cheaper sequencing technologies, has brought into focus the potential of managing weeds in farmlands through direct genetic control approaches, but could be achieved stably or transiently. These approaches encompass a range of technologies that could potentially manipulate expression of key genes in weeds to reduce its fitness and competitiveness, or, by altering the crop to improve its competitiveness or herbicide tolerance. The push for reducing or circumventing the use of chemicals in farmlands has provided an added incentive to develop practical and feasible molecular approaches for weed management, although there are significant technical, practical, and regulatory challenges for utilizing these prospective molecular technologies in weed management.

Herbicide Resistance in Phalaris Species: A Review

Weeds, such as Phalaris spp., can drastically reduce the yield of crops, and the evolution of resistance to herbicides has further exacerbated this issue. Thus far, 23 cases of herbicide resistance in 11 countries have been reported in Phalaris spp., including Phalaris minor Retz., Phalaris paradoxa L., and Phalaris brachystachys L., for photosystem II (PS-II), acetyl-CoA carboxylase (ACCase), and acetolactate synthase (ALS)-inhibiting herbicides. This paper will first review the cases of herbicide resistance reported in P. minor, P. paradoxa, and P. brachystachys. Then, the mechanisms of resistance in Phalaris spp. are discussed in detail. Finally, the fitness cost of herbicide resistance and the literature on the management of herbicide-resistant weeds from these species are reviewed.

Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed (Conyza canadensis)

The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (Conyza canadensis), compared to a susceptible biotype (TNS). A read size of 100.2 M was sequenced on the Illumina platform and subjected to de novo assembly, resulting in 77,072 gene-level contigs, of which 32,493 were uniquely annotated by a BlastX alignment of protein sequence similarity. The most differentially expressed genes were enriched in the gene ontology (GO) term of the transmembrane transport protein. In addition, fifteen upregulated genes were identified in TNR after glyphosate treatment but were not detected in TNS. Ten of these upregulated genes were transmembrane transporter or kinase receptor proteins. Therefore, a combination of changes in gene expression among transmembrane receptor and kinase receptor proteins may be important for endowing non-target-site glyphosate-resistant C. canadensis.

Design, Synthesis, and Herbicidal Activity of Thioether Containing 1,2,4-Triazole Schiff Bases as Transketolase Inhibitors

Transketolase (TK) represents a potential target for novel herbicide development. To discover novel TK inhibitors with potency against resistant weeds, 36 thioether compounds containing 1,2,4-triazole Schiff bases were designed and synthesized for herbicidal activity evaluation. The results demonstrated that compounds 5av and 5aw provided excellent weed control with inhibition of over 90% against the tested weeds, even at concentrations as low as 100 mg/L in vitro. In addition, compounds 5av and 5aw exhibited higher postemergence herbicidal activity than all of the positive controls against the tested weeds at 50-90 g [active ingredient (ai)]/ha in a greenhouse, while being safe for crops of maize and wheat at 90 g (ai)/ha. Fluorescent binding experiments of At TK indicated that compounds 5av and 5aw had strong TK inhibitory activity and could tightly bind with the enzyme At TK. Also, molecular docking analyses revealed that the structures of compounds 5av and 5aw were suitable for TK inhibitory activity. Taken together, these results suggested that compounds 5av and 5aw were promising herbicide candidates for weed control in wheat and maize fields targeting TK.

Into the weeds: new insights in plant stress

Weeds, plants that thrive in the face of disturbance, have eluded human's attempts at control for >12 000 years, positioning them as a unique group of extreme stress tolerators. The most successful weeds have a suite of traits that enable them to rapidly adapt to environments typified by stress, growing in hostile conditions or subject to massive destruction from agricultural practices. Through their ability to persist and adapt, weeds illuminate principles of evolution and provide insights into weed management and crop improvement. Here we highlight why the time is right to move beyond traditional model systems and leverage weeds to gain a deeper understanding of the mechanisms, adaptations, and genetic and physiological bases for stress tolerance.

Phytotoxicity of Schiekia timida Seed Extracts, a Mixture of Phenylphenalenones

Phenylphenalenones, metabolites found in Schiekia timida (Haemodoraceae), are a class of specialized metabolites with many biological activities, being phytoalexins in banana plants. In the constant search to solve the problem of glyphosate and to avoid resistance to commercial herbicides, this work aimed to investigate the phytotoxic effect of the methanolic extract of S. timida seeds. The chemical composition of the seed extract was directly investigated by NMR and UPLC-QToF MS and the pre- and post-emergence phytotoxic effect on a eudicotyledonous model (Lactuca sativa) and a monocotyledonous model (Allium cepa) was evaluated through germination and seedling growth tests. Three concentrations of the extract (0.25, 0.50, and 1.00 mg/mL) were prepared, and four replicates for each of them were analyzed. Three major phenylphenalenones were identified by NMR spectroscopy: 4-hydroxy-anigorufone, methoxyanigorufone, and anigorufone, two of those reported for the first time in S. timida. The presence of seven other phenylphenalenones was suggested by the LC-MS analyses. The phenylphenalenone mixture did not affect the germination rate, but impaired radicle and hypocotyl growth on both models. The effect in the monocotyledonous model was statistically similar to glyphosate in the lowest concentration (0.25 mg/mL). Therefore, although more research on this topic is required to probe this first report, this investigation suggests for the first time that phenylphenalenone compounds may be post-emergence herbicides.

Phytotoxic bioassays and Fingerprinting by HPLC-DAD of Eragrostis plana Nees Root Extracts - application of chemometrics

Eragrostis plana (Nees) (Tough Lovegrass) shows ability to interfere with other plants, a phenomenon known as allelopathy. This chemical interaction between plants occurs due to the release of compounds into the environment. Thus, a phytotoxicity study was carried out with E. plana roots collected during each season throughout the year, and the compounds were extracted with solvents of increasing polarity. The data from the bioassays were analyzed by GLM and PCA. In addition, a fingerprint of these extracts was obtained by HPLC-DAD. The extracts in petroleum ether from roots collected in the winter and summer showed greater phytotoxicity on Ipomoea grandifolia germination and growth. The PCA obtained from the chromatogram of the crude extract showed that the extracts in petroleum ether were chemically different from the extracts in ethyl acetate and methanol. Thus, continuing this study in order to develop a new generation of bio-herbicides is essential.

Assessment of Glyphosate Impact on the Agrofood Ecosystem

Agro-industries should adopt effective strategies to use agrochemicals such as glyphosate herbicides cautiously in order to protect public health. This entails careful testing and risk assessment of available choices, and also educating farmers and users with mitigation strategies in ecosystem protection and sustainable development. The key to success in this endeavour is using scientific research on biological pest control, organic farming and regulatory control, etc., for new developments in food production and safety, and for environmental protection. Education and research is of paramount importance for food and nutrition security in the shadow of climate change, and their consequences in food production and consumption safety and sustainability. This review, therefore, diagnoses on the use of glyphosate and the associated development of glyphosate-resistant weeds. It also deals with the risk assessment on human health of glyphosate formulations through environment and dietary exposures based on the impact of glyphosate and its metabolite AMPA-(aminomethyl)phosphonic acid-on water and food. All this to setup further conclusions and recommendations on the regulated use of glyphosate and how to mitigate the adverse effects.

The impact of different weed management strategies on weed flora of wheat-based cropping systems

The world population will rise in future, which would demand more wheat production to fulfil dietary needs of wheat-dependent population of the world. Food security in wheat-dependent regions will greatly rely on wheat productivity. Weed infestation is a major constraint reducing wheat productivity globally. Nonetheless, cropping systems and weed management strategies strongly influence weed infestation in modern agriculture. Herbicides are the key weed management tool in conventional agriculture. However, frequent use of herbicides have resulted in the evolution of herbicide-resistance weeds, which made weed management a challenging task. Sustainable and eco-friendly weed management strategies shift weed-crop competition in the favour of crop plants. Limited studies have evaluated the interactive effect of cropping systems and weed management strategies on weed flora of wheat-based cropping systems (WBCSs). This two-year study evaluated the impact of different weed management strategies (WMSs) on weed flora of WBCSs, i.e., fallow-wheat (FW), rice-wheat (RW), cotton-wheat (CW), mungbean-wheat (MW) and sorghum-wheat (SW). The WMSs included in the study were, false seedbed, allelopathic water extracts and herbicide application, while weed-free and weedy-check were maintained as control treatments. Data relating to diversity and density of individual and total broadleaved and narrow-leaved weeds were recorded. The WBCSs, WMSs and their interaction significantly altered diversity and density of individual, total, broadleaved and narrow-leaved weeds. Weed-free and weedy-check treatments recorded the lowest and the highest values of diversity and density of individual, total, broadleaved and narrow-leaved weeds. Herbicide application effectively reduced density and diversity of weeds. Allelopathic water extracts and false seedbed proved less effective than herbicides. On the other hand, SW cropping system not only reduced weed density but also limited the weed flora. It is concluded that false seedbed and SW cropping system can be efficiently used to manage weeds in WBCSs. However, long-term studies are needed to infer the impact of SW cropping system and false seedbed on soil properties, soil microbes and productivity of wheat crop.

Evaluation of Dittrichia viscosa (L.) Greuter Dried Biomass for Weed Management

Dittrichia viscosa (L.) Greuter, a plant species common in the Mediterranean basin, produces several bioactive compounds, some of which have herbicidal effects. A number of greenhouse and field experiments were carried out in order to evaluate if these effects could be obtained also by using the whole plant biomass, to identify the efficacious doses, determine their effects on seed germination and weed emergence, and to evaluate influence of soil characteristics on biomass efficacy. The experiments carried out evidenced that: (i) the dried biomass completely hampers plant emergence when high doses (30–40 kg biomass m⁻³ of soil) are mixed into the soil, or delays it at a lower dose (10 kg m⁻³); (ii) the detrimental effects are not affected by soil type. The exploitation of the D. viscosa dried biomass appears to be a feasible option in weed management practices and its potential is discussed.

Phytotoxic Neocassane Diterpenes from Eragrostis plana

Five new neocassane-like diterpenes (1-5) were isolated from the roots of Eragrostis plana. Their structures were elucidated by spectroscopic data, and the absolute configurations of the representative compounds neocassa-12(17),15-dien-3-one (2) and neocassa-12(13),15-diene-3,14-dione (5) were assigned by vibrational circular dichroism. The phytotoxic activity of compounds 3, 4, and 5 was evaluated against the germination and growth of Ipomoea grandifolia and Euphorbia heterophylla. Compound 4 exhibited the most potent activity for growth variables, resulting in the smallest radicle length of I. grandifolia and in the smallest aerial part length of E. heterophylla. Compound 5 reduced the germination speed index more effectively than the herbicide glyphosate (Roundup).

Synthetic auxin herbicides: finding the lock and key to weed resistance

Synthetic auxin herbicides are designed to mimic indole-3-acetic acid (IAA), an integral plant hormone affecting cell growth, development, and tropism. In this review, we explore target site genes in the auxin signaling pathway including SCF^TIR1/AFB, Aux/IAA, and ARFs that are confirmed or proposed mechanisms for weed resistance to synthetic auxin herbicides. Resistance to auxin herbicides by metabolism, either by enhanced cytochrome P450 detoxification or by loss of pro-herbicide activation, is a major non-target-site resistance pathway. We speculate about potential fitness costs of resistance due to effects of resistance-conferring mutations, provide insight into the role of polyploidy in synthetic auxin resistance evolution, and address the genetic resources available for weeds. This knowledge will be the key to unlock the long-standing questions as to which components of the auxin signaling pathway are most likely to have a role in resistance evolution. We propose that an ambitious research effort into synthetic auxin herbicide/target site interactions is needed to 1) explain why some synthetic auxin chemical families have activity on certain dicot plant families but not others and 2) fully elucidate target-site cross-resistance patterns among synthetic auxin chemical families to guide best practices for resistance management.