Overview of glyphosate-resistant weeds worldwide

Target-Site Mutations Conferring Herbicide Resistance

Mutations conferring evolved herbicide resistance in weeds are known in nine different herbicide sites of action. This review summarizes recently reported resistance-conferring mutations for each of these nine target sites. One emerging trend is an increase in reports of multiple mutations, including multiple amino acid changes at the glyphosate target site, as well as mutations involving two nucleotide changes at a single amino acid codon. Standard reference sequences are suggested for target sites for which standards do not already exist. We also discuss experimental approaches for investigating cross-resistance patterns and for investigating fitness costs of specific target-site mutations.

Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance

The human-directed, global selection for glyphosate resistance in weeds has revealed a fascinating diversity of evolved resistance mechanisms, including herbicide sequestration in the vacuole, a rapid cell death response, nucleotide polymorphisms in the herbicide target (5-enolpyruvylshikimate-3-phosphate synthase, EPSPS) and increased gene copy number of EPSPS. For this latter mechanism, two distinct molecular genetic mechanisms have been observed, a tandem duplication mechanism and a large extrachromosomal circular DNA (eccDNA) that is tethered to the chromosomes and passed to gametes at meiosis. These divergent mechanisms have a range of consequences for the spread, fitness, and inheritance of resistance traits, and, particularly in the case of the eccDNA, demonstrate how evolved herbicide resistance can generate new insights into plant adaptation to contemporary environmental stress.

Inflammatory Effects of Subacute Exposure of Roundup in Rat Liver and Adipose Tissue

Roundup is a popular herbicide containing glyphosate as an active ingredient. The formulation of Roundup is speculated to have critical toxic effects, one among which is chronic inflammation. The present study analyzed adverse inflammatory effects in the liver and adipose tissue of rats after a subacute exposure of Roundup. Adult male rats were exposed to various doses of Roundup (0, 5, 10, 25, 50, 100 and 250 mg/kg bodyweight [bw] glyphosate) orally, everyday for 14 days. On day 15, liver and adipose tissues from dosed rats were analyzed for inflammation markers. C-reactive protein in liver, cytokines IL-1β, TNF-α, IL-6, and inflammatory response marker, and prostaglandin–endoperoxide synthase were upregulated in liver and adipose of rats exposed to higher (100 and 250 mg/kg bw/d) doses of Roundup. Cumulatively, our data suggest development of inflammation in lipid and hepatic organs upon exposure to Roundup. Furthermore, liver histological studies showed formation of vacuoles, fibroid tissue, and glycogen depletion in the groups treated with doses of higher Roundup. These observations suggest progression of fatty liver disease in Roundup-treated adult rats. In summary, our data suggest progression of multiorgan inflammation, liver scarring, and dysfunction post short-term exposure of Roundup in adult male rats.

How protoporphyrinogen IX oxidase inhibitors and transgenesis contribute to elucidate plant tetrapyrrole pathway

Several families of herbicides, especially diphenyl ether (DPE) and pyrimidinedione, target the plant tetrapyrrole biosynthesis pathways and in particular one key enzyme, protoporphyrinogen IX oxidase (PPO). When plants are treated with DPE or pyrimidinedione, an accumulation of protoporphyrin IX, the first photosensitizer of this pathway, is observed in cytosol where it becomes very deleterious under light. Indeed these herbicides trigger plant death in two distinct ways: (i) inhibition of chlorophylls and heme syntheses and (ii) a huge accumulation of protoporphyrin IX in cytosol. Recently, a strategy based on plant transgenesis that induces deregulation of the tetrapyrrole pathway by up- or down-regulation of genes encoding enzymes, such as glutamyl-[Formula: see text]RNA reductase, porphobilinogen deaminase and PPO, has been developed. Against all expectations, only transgenic crops overexpressing PPO showed resistance to DPE and pyrimidinedione. This herbicide resistance of transgenic crops leads to the hypothesis that the overall consumption of herbicides will be reduced as previously reported for glyphosate-resistant transgenic crops. In this review, after a rapid presentation of plant tetrapyrrole biosynthesis, we show how only PPO enzyme can be the target of DPE and how transgenic crops can be further resistant not only to herbicide but also to abiotic stress such as drought or chilling. Keeping in mind that this approach is mostly prohibited in Europe, we attempt to discuss it to interest the scientific community, from plant physiologists to chemists, who work on the interface of photosensitizer optimization and agriculture.

The Triple Amino Acid Substitution TAP-IVS in the EPSPS Gene Confers High Glyphosate Resistance to the Superweed Amaranthus hybridus

The introduction of glyphosate-resistant (GR) crops revolutionized weed management; however, the improper use of this technology has selected for a wide range of weeds resistant to glyphosate, referred to as superweeds. We characterized the high glyphosate resistance level of an Amaranthus hybridus population (GRH)-a superweed collected in a GR-soybean field from Cordoba, Argentina-as well as the resistance mechanisms that govern it in comparison to a susceptible population (GSH). The GRH population was 100.6 times more resistant than the GSH population. Reduced absorption and metabolism of glyphosate, as well as gene duplication of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) or its overexpression did not contribute to this resistance. However, GSH plants translocated at least 10% more 14C-glyphosate to the rest of the plant and roots than GRH plants at 9 h after treatment. In addition, a novel triple amino acid substitution from TAP (wild type, GSH) to IVS (triple mutant, GRH) was identified in the EPSPS gene of the GRH. The nucleotide substitutions consisted of ATA102, GTC103 and TCA106 instead of ACA102, GCG103, and CCA106, respectively. The hydrogen bond distances between Gly-101 and Arg-105 positions increased from 2.89 Å (wild type) to 2.93 Å (triple-mutant) according to the EPSPS structural modeling. These results support that the high level of glyphosate resistance of the GRH A. hybridus population was mainly governed by the triple mutation TAP-IVS found of the EPSPS target site, but the impaired translocation of herbicide also contributed in this resistance.

A novel triple amino acid substitution in the EPSPS found in a high-level glyphosate-resistant Amaranthus hybridus population from Argentina

BACKGROUND

The evolution of herbicide-resistant weeds is one of the most important concerns of global agriculture. Amaranthus hybridus L. is a competitive weed for summer crops in South America. In this article, we intend to unravel the molecular mechanisms by which an A. hybridus population from Argentina has become resistant to extraordinarily high levels of glyphosate.

RESULTS

The glyphosate-resistant population (A) exhibited particularly high parameters of resistance (GR50  = 20 900 g ai ha-1 , Rf = 314), with all plants completing a normal life cycle even after 32X dose application. No shikimic acid accumulation was detected in the resistant plants at any of the glyphosate concentrations tested. Molecular and genetic analyses revealed a novel triple substitution (TAP-IVS: T102I, A103V, and P106S) in the 5-enol-pyruvylshikimate-3-phosphate synthase (EPSPS) enzyme of population A and an incipient increase on the epsps relative copy number but without effects on the epsps transcription levels. The novel mechanism was prevalent, with 48% and 52% of the individuals being homozygous and heterozygous for the triple substitution, respectively. In silico conformational studies revealed that TAP-IVS triple substitution would generate an EPSPS with a functional active site but with an increased restriction to glyphosate binding.

CONCLUSION

The prevalence of the TAP-IVS triple substitution as the sole mechanism detected in the highly glyphosate resistant population suggests the evolution of a new glyphosate resistance mechanism arising in A. hybridus. This is the first report of a naturally occurring EPSPS triple substitution and the first glyphosate target-site resistance mechanism described in A. hybridus. © 2018 Society of Chemical Industry.

Characterization of 4-hydroxyphenylpyruvate dioxygenases, inhibition by herbicides and engineering for herbicide tolerance in crops

4-Hydroxyphenylpyruvate dioxgenase (HPPD) enzymes from rat and from several plants contained only about a single inhibitor-binding active site per dimer which matched the content of iron in the purified Arabidopsis thaliana and Avena sativa enzymes. The dimeric HPPDs were about 10 fold more catalytically active than the tetrameric P. fluorescens enzyme with k_cat/K_mHPP values ranging from 0.8 to 2.5 s^-1 μM^-1. Most were also highly sensitive to herbicides with, for example, K_i values for mesotrione ranging from 25 to 100 pM. Curiously HPPDs from cool climate grasses were much less herbicide-sensitive. When likewise expressed in Nicotinia tabacum, Avena sativa HPPD, K_i value of 11 nM for mesotrione, conferred far greater tolerance to mesotrione (Callisto^TM) than did any of the more sensitive HPPDs. Targeted mutagenesis of the Avena HPPD led to the discovery of 4 mutations imparting improved inherent tolerance, defined as the ratio of K_i to K_mHPP, by about 16 fold without any loss of catalytic activity. The Nicotinia line with the highest expression of this quadruple mutant exhibited substantial resistance even up to a 3 kg/ha post-emergence application of mesotrione. The maximum observed expression level of heterologous plant HPPDs in tobacco was ca. 0.35% of the total soluble protein whereas the endogenous tobacco HPPD constituted only ca. 0.00075%. At such high expression even HPPDs with impaired catalytic activity could be effective. A quintuple mutant Avena sativa HPPD conferred substantial tolerance across a broad range of HPPD herbicide chemistries despite being only ca. 5 % as catalytically active as the wild type enzyme. Testing various wild type and mutant HPPDs in tobacco revealed that tolerance to field rates of herbicide generally requires about two order of magnitude increases in both inherent herbicide tolerance and expression relative to endogenous levels. This double hurdle may explain why target-site based resistance to HPPD-inhibiting herbicides has been slow to evolve in weeds.

Recent developments in metabolomics-based research in understanding transgenic grass metabolism

BACKGROUND

Transgenic herbicide-resistant (HR) turfgrass together with its associated, broad spectrum herbicides promise cheap, selective and efficient weed control by excluding infested weeds resulting in turf lawn with high uniformity and aesthetic value. The concept of this "weeding program" initiated from modern biotechnology has been widely implemented in several principal crops including maize, soybean, canola and cotton as early as the 1990s. Transgenic HR turfgrass classified as a genetically modified organism (GMO) has undoubtedly caused public concern with respect to its biosafety and legalities similar to well-established HR crops. Nevertheless, applying metabolomics-based approaches which focuses on the identification of the global metabolic state of a biological system in response to either internal or external stimuli can also provide a comprehensive characterization of transgenic grass metabolism and its involvement in biosecurity and public perception.

AIM OF REVIEW

This review summaries the recent applications of metabolomics applied to HR crops to predict the molecular and physiological phenotypes of HR turfgrass species, glyphosate-resistant Kentucky bluegrass (Poa pratensis L.) and glufosinate-resistant creeping bentgrass (Agrotis stonifera L.). Additionally, this review also presents background knowledge with respect to the application of metabolomics, transformation of HR crops and its biosafety concerns, turfgrass botanical knowledge and its economic and aesthetic value.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The purpose of this review is to demonstrate the molecular and physiological phenotypes of HR turfgrass based on several lines of evidence primarily derived from metabolomics data applied to HR crops to identify alterations on HR turfgrass metabolism as a result of genetic modification that confers resistant traits.

Characterization of three glyphosate resistant Parthenium hysterophorus populations collected in citrus groves from Mexico

Continuous use of glyphosate in citrus groves in the Gulf of Mexico region has selected for resistant Parthenium hysterophorus L. populations. In this study, the target-site and non-target-site resistance mechanisms were characterized in three putative glyphosate-resistant (GR) P. hysterophorus populations, collected in citrus groves from Acateno, Puebla (GR1 and GR2) and Martínez de la Torre, Veracruz (GR3), and compared with a susceptible population (GS). Based on plant mortality, the GR populations were 9.2-17.3 times more resistant to glyphosate than the GS population. The low shikimate accumulation in the GR population confirmed this resistance. Based on plant mortality and shikimate accumulation, the GR3 population showed intermediate resistance to glyphosate. The GR populations absorbed 15-28% less 14C-glyphosate than the GS population (78.7% absorbed from the applied) and retained 48.7-70.7% of 14C-glyphosate in the treated leaf, while the GS population translocated ~68% of absorbed herbicide to shoots and roots. The GR3 population showed the lowest translocation and absorption rates, but was found to be susceptible at the target site level. The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene sequence of the GR1 and GR2 populations showed the Pro106-Ser mutation, conferring 19- and 25-times more resistance in comparison to the GS population, respectively. Reduced absorption and impaired translocation conferred glyphosate resistance on the GR3 population, and contributed partially to the resistance of the GR1 and GR2 populations. Additionally, the Pro-106-Ser mutation increased the glyphosate resistance of the last two P. hysterophorus populations.

Trends in the Use of Glyphosate Herbicide and Its Relevant Regulations in Taiwan: A Water Contaminant of Increasing Concern

In Taiwan and other countries, glyphosate has been used widely as a non-selective herbicide over 40 years in crop lands and non-crop lands. However, public concerns about its environmental and health risks have increased rapidly because the International Agency for Research on Cancer (IARC) reclassified it as Group 2A (probably carcinogenic to humans) in 2015. From the viewpoints of environmental quality, food security and human health, it is necessary to regulate the release of glyphosate into the environment due to its massive use. The purpose of this case study was to analyze the historical consumption of glyphosate in Taiwan and also summarize its current regulatory measures through multi-ministerial levels. It showed that the sales quantities of glyphosate in Taiwan can be grouped into three stages, which include a ramping period (1984⁻1992), a stable period (1992⁻2007), and a declining period (2007⁻2016). These variations can be correlated with the annual price, manufacturers' promotion and other non-selective herbicide competitors (i.e., paraquat and glufosinate), as well as the excellent action features of glyphosate. It should be noted that its sales quantities significantly increased from 3200 metric tons in 2015 to 4535 metric tons in 2016 mainly due to the official announcement of paraquat ban effective in February 2019. The core regulations for protecting food security and water quality from the use of glyphosate are based on its residual limits and standards under the authorization of the Food Sanitation Management Act (FSMA) and the Water Pollution Control Act (WPCA), respectively. More importantly, there are occasional reports of contamination by herbicides (including glyphosate) in drinking water sources. Unfortunately, glyphosate is not yet considered among chemical items when evaluating drinking water quality standards in Taiwan.

Viewing evidence of harm accompanying uses of glyphosate-based herbicides under US legal requirements

Some epidemiological experts feel there is sufficient proof that glyphosate use adversely affects human health, and glyphosate has been labeled as probably carcinogenic by the International Agency for Research on Cancer. Federal law in the United States provides two major options under which health concerns about glyphosate use might be addressed. First, registrations of glyphosate-based herbicides (GBHs) need to be cancelled if the costs are greater that its benefits. Since the cancellation of GBH registrations in the United States would lead to higher maize and soybean prices that would adversely affect food security, further analyses are needed. Second, US law requires consideration of the human dietary risk from pesticide residues, and tolerances of allowable amounts of glyphosate residues allowed to remain in or on food items have been established. Social cost curves depicting three options for regulating GBHs show preferred strategies dependent upon the magnitude of adverse effects on human health and food insecurity. Measures to reduce harm to humans can be identified to ameliorate health damages to allow some uses of GBHs to continue, but only if the evidence supports the conclusion that "no harm will result from aggregate exposure to the pesticide chemical residue."

Carfentrazone-ethyl and glyphosate drift inhibits uredinial formation of Austropuccinia psidii on Eucalyptus grandis leaves

BACKGROUND

The response to infection of Austropuccinia psidii in resistant (CLR-383) and susceptible (CLR-384) Eucalyptus grandis clones, exposed to herbicide drift of carfentrazone-ethyl, glyphosate and a mixture of these two herbicides, was evaluated at microscopic and physiological levels.

RESULTS

Plants of the two clones showed symptoms of phytotoxicity caused by herbicide drift. However, net CO2 assimilation rate, height and shoot dry matter were lower in CLR-384 than in CLR-383. At the ultrastructure level, the leaves of both clones exposed to the herbicides showed thylakoid disorganization and accumulation of starch grains in the chloroplasts. Only plants of CLR-384 were infected by A. psidii, but when exposed to herbicide drift, rust severity was lower than in control plants. Six days after inoculation (dai), plants of this clone exposed to the herbicides had smaller uredinia than control plants. At 12 dai, non-herbicide treated plants showed normal uredinia, containing abundant urediniospores. By contrast, plants exposed to the herbicides were less colonized by the fungus, and the uredinia were smaller with reduced production of urediniospores, which were sometimes not even detected.

CONCLUSION

Glyphosate and carfentrazone-ethyl herbicide drift reduce infection and uredinial formation of A. psidii and to some extent induce basal resistance in a susceptible clone of E. grandis. © 2018 Society of Chemical Industry.

Genomic Clues for Crop-Weed Interactions and Evolution

Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop-weed interactions that reveal several major evolutionary innovations such as de-domestication, interactions mediated by allelochemical secondary metabolites, and parasitic genetic elements that play crucial roles in enhancing weed invasiveness in agricultural settings. We believe that these key studies will guide future research into the evolution of crop-weed interactions, and further the development of practical applications in agricultural weed control and crop breeding.

Improving soil seed bank management

Problems associated with simplified weed management motivate efforts for diversification. Integrated weed management uses the fundamentals of weed biology and applied ecology to provide a framework for diversified weed management programs; the soil seed bank comprises a necessary part of this framework. By targeting seeds, growers can inhibit the propagule pressure on which annual weeds depend for agricultural invasion. Some current management practices affect weed seed banks, such as crop rotation and tillage, but these tools are often used without specific intention to manage weed seeds. Difficulties quantifying the weed seed bank, understanding seed bank phenology, and linking seed banks to emerged weed communities challenge existing soil seed bank management practices. Improved seed bank quantification methods could include DNA profiling of the soil seed bank, mark and recapture, or 3D LIDAR mapping. Successful and sustainable soil seed bank management must constrain functionally diverse and changing weed communities. Harvest weed seed controls represent a step forward, but over-reliance on this singular technique could make it short-lived. Researchers must explore tools inspired by other pest management disciplines, such as gene drives or habitat modification for predatory organisms. Future weed seed bank management will combine multiple complementary practices that enhance diverse agroecosystems. © 2018 Society of Chemical Industry.

Weed responses to fallow management in Pacific Northwest dryland cropping systems

A two-year rotation of summer fallow (SF)/winter wheat (WW) is the most common cropping system in low precipitation areas of the U.S. Pacific Northwest (PNW). In SF, multiple tillage operations are used to manage weeds and maximize soil water storage and potential WW yield. Reduced tillage fallow (RTF) is an alternative to SF that leaves >30% of the previous crop's residue on the surface. A four-year (2014-18) field study was conducted to evaluate the influence of SF and RTF on weed species density, cover and composition in dryland WW; determine if changes in these weed infestation attributes have any influence on crop density and yield; and evaluate economic costs of each type of fallow management. The experimental design was randomized complete block with four replications where each phase of SF/WW and RTF/WW rotations was present every year. Individual plots of WW were divided into a weedy sub-plot with no weed control, general area with chemical weed control, and weed-free sub-plot where weeds were manually removed. Infestations of annual grass and other weeds in weedy sub-plots increased throughout the study. Grass weed cover, consisting mainly of downy brome (Bromus tectorum L.), and total weed cover were significantly lower in WW following RTF than following SF in all years except 2018. Densities of grass and total weeds were similar in both fallow managements indicating that weed plants were larger in WW following SF than following RTF due to earlier or faster emergence. Grass cover differences were not found in general areas likely because of a reduced seedbank. When weeds were present, mean yield of WW was higher following RTF than SF indicating that weeds were less competitive in RTF. Reduced tillage fallow could improve weed management in fallow/WW cropping systems of the PNW compared to SF/WW, particularly if the most problematic species are grasses.

The Development of Macrophomina phaseolina (Fungus) Resistant and Glufosinate (Herbicide) Tolerant Transgenic Jute

The worldwide demand for natural bast fibers is met aptly by the long, golden and silky fibers of jute. This highest bast fiber producing crop is of great applicability and is extensively used in paper and textile industry. Macrophomina phaseolina (Tassi) Goid is a severely devastating necrotrophic fungal pathogen causing stem rot, root rot, and charcoal rot diseases in both the cultivated species of jute - Corchorus capsularis and Corchorus olitorius. Another major problem faced in jute cultivation is profuse weed infestation in the fields. Huge losses in quality fiber production is caused by this pathogenic fungi and cultivation cost increases as well due to weed management expenditure during cropping season. To solve these long persisting jute cultivation challenges, the chitinase (chi11) gene (to provide fungus resistance) and the bar gene (to provide herbicide tolerance) have been incorporated in C. capsularis JRC-321 via Agrobacterium transformation and analyzed up to T2 generation. Stable integration and expression of these two genes in the jute genome was confirmed upon extensive analyses. Transgenic plants showed higher chitinase expression and chitin degrading activity than non-transgenic control plants. Antifungal activity significantly increased in transgenic plants as confirmed by detached leaf and whole plant M. phaseolina bioassay. Herbicide tolerance was analyzed by growing transgenic plants in 10 mg/l glufosinate ammonium containing media and by spraying 0.25% (v/v) glufosinate herbicide Basta® on them. Assessment of residual phytotoxicity effects of Basta® on soil confirmed no negative impact on growth of indicator plants corn and cucumber. Transgenic jute plants were at par with non-transgenic (control) jute plants in all phenotypic aspects. Non-transgenic (control) jute plants suffered significant losses in fiber yield and quality due to M. phaseolina infection whereas the transgenic lines maintained the quality of fiber even after the infection.