Do plants pay a fitness cost to be resistant to glyphosate?

Translating weighted probabilistic bits to synthetic genetic circuits

Synthetic genetic circuits in plants could be the next technological horizon in plant breeding, showcasing potential for precise patterned control over expression. Nevertheless, uncertainty in metabolic environments prevents robust scaling of traditional genetic circuits for agricultural use, and studies show that a deterministic system is at odds with biological randomness. We analyze the necessary requirements for assuring Boolean logic gate sequences can function in unpredictable intracellular conditions, followed by interpreted pathways by which a mathematical representation of probabilistic circuits can be translated to biological implementation. This pathway is utilized through translation of a probabilistic circuit model presented by Pervaiz that works through a series of bits; each composed of a weighted matrix that reads inputs from the environment and a random number generator that takes the matrix as bias and outputs a positive or negative signal. The weighted matrix can be biologically represented as the regulatory elements that affect transcription near promotors, allowing for an electrical bit to biological bit translation that can be refined through tuning using invertible logic prediction of the input to output relationship of a genetic response. Failsafe mechanisms should be introduced, possibly through the use of self-eliminating CRISPR-Cas9, dosage compensation, or cybernetic modeling (where CRISPR is clustered regularly interspaced short palindromic repeats and Cas9 is clustered regularly interspaced short palindromic repeat-associated protein 9). These safety measures are needed for all biological circuits, and their implementation is needed alongside work with this specific model. With applied responses to external factors, these circuits could allow fine-tuning of organism adaptation to stress while providing a framework for faster complex expression design in the field.

Bifunctional Phenylalanine/Tyrosine Ammonia-Lyase (PTAL) Enhances Lignin Biosynthesis: Implications in Carbon Fixation in Plants by Genetic Engineering

Lignin is a key metabolite for terrestrial plants. Two types of aromatic amino acids, phenylalanine (Phe) and tyrosine (Tyr), serve as the precursors for lignin biosynthesis. In most plant species, Phe is deaminated by Phe ammonia-lyase (PAL) to initiate lignin biosynthesis, but in grass species, Phe and Tyr are deaminated by Phe/Tyr ammonia-lyase (PTAL). To understand the efficiency of PAL and PTAL, we used transgenic and non-transgenic Arabidopsis with PAL and crop-weedy rice hybrids (CWRH) with PTAL to analyze lignin-biosynthesis-associated metabolites. The transgenic plants overexpressed the exogenous 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, whereas the non-transgenic plants normally expressed the endogenous EPSPS gene. Our results show significantly increased Phe/Tyr contents in transgenic Arabidopsis and CWRH plants, leading to substantially increased lignin and biomass. In addition, the PTAL pathway promotes a much greater proportion of increased lignin and biomass in transgenic CWRH than in transgenic Arabidopsis lineages. Evidently, more efficient lignin biosynthesis characterized the grass species possessing the PTAL pathway. These findings are important for a better understanding of the PAL and PTAL's functions in the phenylpropanoid metabolic pathways in the evolution of plant species. These findings also have great value for implications such as effective carbon fixation by enhancing lignin biosynthesis through genetic engineering of their key genes in appropriately selected plant species.

Regional evaluation of glyphosate pollution in the minor irrigation network

Due to its low cost, its ease of use and to the "mild action" declared for long time by the Control and Approval Agencies towards it, the herbicide Glyphosate, is one of the currently best-selling and most-used agricultural products worldwide. In this work, we evaluated the presence and spread of Glyphosate in the Po River Basin (Northern Italy), one of the regions with the most intensified agriculture in Europe and where, by now for decades, a strong and general loss of aquatic biodiversity is observed. In order to carry out a more precise study of the real presence of this herbicide in the waters, samples were collected from the minor water network for two consecutive years, starting in 2022, at an interval time coinciding with those of the spring and summer crop treatments. In contrast to the sampling strategies generally adopted by Environmental Protection Agencies, a more focused sampling strategy was adopted to highlight the possible high concentrations in minor watercourses in direct contact with cultivated fields. Finally, we investigated the possible consequences that the higher amounts of Glyphosate found in our monitoring activities can have on stress reactions in plant (Groenlandia densa) and animal (Daphnia magna) In all the monitoring campaigns we detected exceeding European Environmental Quality Standard - EQS limits (0.1 μg/L) values. Furthermore, in some intensively agricultural areas, concentrations reached hundreds of μg/L, with the highest peaks during spring. In G. densa and D. magna, the exposition to increasing doses of herbicide showed a clear response linked to metabolic stress. Overall, our results highlight how, after several decades of its use, the Glyphosate use efficiency is still too low, leading to economic losses for the farm and to strong impacts on ecosystem health. Current EU policy indications call for an agroecological approach necessary to find alternatives to chemical weed control, which farms can develop in different contexts in order to achieve the sustainability goals set by the Farm to Fork strategy.

Herbicide resistance evolution, fitness cost, and the fear of the superweeds

Despite considerable differences in cropping systems around the globe, chemical weed control is a key tool in conventional agroecosystems, which has led to an increase in herbicide resistance. Although mutations causing resistance are thought to have an adaptation cost in resistant plants compared to the susceptible ones under herbicide-free conditions, such cost may not always express or will express under certain ecological conditions. To ensure that herbicides will keep going as viable instruments in agricultural production, strategies to minimize resistance are needed. Proactive or reactive strategies for weed control should utilize an overall integrated weed management approach by combining as many weed management practices as possible. The term 'superweed' was used initially to describe the phenomenon in which genetically engineered crops would become troublesome weeds and that the genes of interest would spread into related weeds, rendering them problematic, or into wild species, turning them into troublesome weeds. Contrary to the above definition, the use of this term in the literature has often been linked with herbicide resistance, mostly related to the cultivation of genetically engineered crops and the related increase in the use of glyphosate, which rapidly selected resistant weed populations. From a scientific point of view, weeds are better survivors than non-weedy species and cause crop problems because they have several unique traits, e.g., they are aggressive, adapt easily to different environments, produce many seeds, compete strongly with crops, disperse easily, are difficult to control, traits which occur whether weeds are herbicide-resistant or not. We propose that the term 'superweed' should be referred to weeds with resistant populations to several herbicides with diverse modes of action (MOAs).

A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)

Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.

The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates

Glyphosate (GS) inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that is required for aromatic amino acid, folate and quinone biosynthesis in Bacillus subtilis and Escherichia coli. The inhibition of the EPSP synthase by GS depletes the cell of these metabolites, resulting in cell death. Here, we show that like the laboratory B. subtilis strains also environmental and undomesticated isolates adapt to GS by reducing herbicide uptake. Although B. subtilis possesses a GS-insensitive EPSP synthase, the enzyme is strongly inhibited by GS in the native environment. Moreover, the B. subtilis EPSP synthase mutant was only viable in rich medium containing menaquinone, indicating that the bacteria require a catalytically efficient EPSP synthase under nutrient-poor conditions. The dependency of B. subtilis on the EPSP synthase probably limits its evolvability. In contrast, E. coli rapidly acquires GS resistance by target modification. However, the evolution of a GS-resistant EPSP synthase under non-selective growth conditions indicates that GS resistance causes fitness costs. Therefore, in both model organisms, the proper function of the EPSP synthase is critical for the cellular viability. This study also revealed that the uptake systems for folate precursors, phenylalanine and tyrosine need to be identified and characterized in B. subtilis.

Phytochemical Cue for the Fitness Costs of Herbicide-Resistant Weeds

Despite increasing knowledge of the fitness costs of viability and fecundity involved in the herbicide-resistant weeds, relatively little is known about the linkage between herbicide resistance costs and phytochemical cues in weed species and biotypes. This study demonstrated relative fitness and phytochemical responses in six herbicide-resistant weeds and their susceptible counterparts. There were significant differences in the parameters of viability (growth and photosynthesis), fecundity fitness (flowering and seed biomass) and a ubiquitous phytochemical (-)-loliolide levels between herbicide-resistant weeds and their susceptible counterparts. Fitness costs occurred in herbicide-resistant Digitaria sanguinalis and Leptochloa chinensis but they were not observed in herbicide-resistant Alopecurus japonicas, Eleusine indica, Ammannia arenaria, and Echinochloa crus-galli. Correlation analysis indicated that the morphological characteristics of resistant and susceptible weeds were negatively correlated with (-)-loliolide concentration, but positively correlated with lipid peroxidation malondialdehyde and total phenol contents. Principal component analysis showed that the lower the (-)-loliolide concentration, the stronger the adaptability in E. crus-galli and E. indica. Therefore, not all herbicide-resistant weeds have fitness costs, but the findings showed several examples of resistance leading to improved fitness even in the absence of herbicides. In particular, (-)-loliolide may act as a phytochemical cue to explain the fitness cost of herbicide-resistant weeds by regulating vitality and fecundity.

Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate

Gene mutation is a basic evolutionary mechanism in plants under selection pressure of herbicides. Such mutation has pleiotropic effects on plant growth. We systemically investigated the effects of Pro106Leu (P106L), Pro106Ser (P106S), and Thr102Ile + Pro106Ser (TIPS) mutations on EPSPS functionality and fitness traits in Eleusine indica at the biochemical and physiological levels. The affinity of natural EPSPS for glyphosate was 53.8 times higher than that for phosphoenolpyruvate (PEP), as revealed by the dissociation constant; the constant decreased in both the P106L (39.9-fold) and P106S (46.9-fold) mutants but increased in the TIPS (87.5-fold) mutant. The Km (PEP) values of the P106L, P106S, and TIPS mutants were 2.4-, 0.7-, and 4.1-fold higher than that of natural EPSPS, corresponding to resistance levels of 2.5, 1.9, and 11.4, respectively. The catalytic efficiency values (maximum reaction rates) were 0.89-, 0.94-, and 0.26-fold higher than that of natural EPSPS. The levels of metabolites related to amino acids and nucleotides were significantly reduced in the mutated plants. The fitness costs were substantial for the biomass, total leaf area, seed number, and seedling emergence throughout the growth period in the plants with P106L and TIPS mutations. These results provide insights into EPSPS kinetics and their effect on plant growth.

Global Metabolome of Palmer Amaranth (Amaranthus palmeri) Populations Highlights the Specificity and Inducibility of Phytochemical Responses to Abiotic Stress

Commonalities in adaptive responses to abiotic stressors could contribute to the development of cross-resistance in weeds. The degree to which herbicide-induced changes in weeds parallel those induced by other abiotic stress remains unknown. We investigated the specificity of metabolic perturbations induced by glyphosate and drought across three glyphosate-resistant (GR) and two glyphosate-susceptible (GS) biotypes of Palmer amaranth (Amaranthus palmeri) using global metabolomics approaches. Compared to GS-biotypes, in the absence of stress, the GR-biotypes had a higher abundance of primary metabolites, including sugars, nonaromatic amino acids, and organic acids. However, despite having a higher 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene copy number that could upregulate the phenylpropanoid metabolism, the nonstressed GR-biotypes were less abundant in specialized (secondary) metabolites. Under glyphosate stress, 80% of metabolites, including shikimate, that accumulated in GS-biotypes also increased in the GR-biotypes. However, glyphosate triggered the preferential accumulation of glycosides of dihydroxylated and methoxylated flavanols with higher antioxidant potential, and ferulic acid derivatives, specifically in GR-biotypes. The disruption of the shikimate pathway and the accumulation of phenylpropanoids upon glyphosate exposure suggest that the stress response of GR-biotypes could be partly induced. This differential response was less evident in other phytochemical classes and under drought, highlighting that the phytochemical responses are stress-specific rather than biotype-specific.

Challenging glyphosate resistance EPSPS P106S and TIPS mutations with soybean competition and glyphosate: implications for management

BACKGROUND

Eleusine indica (L.) Gaertn. (goosegrass) is a major weed in global cropping systems. It has evolved resistance to glyphosate due to single Pro-106-Ser (P106S) or double Thr-102-Ile + Pro-106-Ser (TIPS) EPSPS target site mutations. Here, experiments were conducted to evaluate the single effect of soybean competition and its combined effect with a glyphosate field dose (1080 g ae ha^-1 ) on the growth and fitness of plants carrying these glyphosate resistance endowing target site mutations.

RESULTS

TIPS E. indica plants are highly glyphosate-resistant but the double mutation endows a substantial fitness cost. The TIPS fitness penalty increased under the effect of soybean competition resulting in a cost of 95%, 95% and 96% in terms of, respectively, vegetative growth, seed mass and seed number investment. Glyphosate treatment of these glyphosate-resistant TIPS plants showed an increase in growth relative to those without glyphosate. Conversely, for the P106S moderate glyphosate resistance mutation, glyphosate treatment alone reduced survival rate, vegetative growth, aboveground biomass (34%), seed mass (48%) and number (52%) of P106S plants relative to the glyphosate nontreated plants. However, under the combined effects of both soybean competition and the field-recommended glyphosate dose, vegetative growth, aboveground biomass, seed mass and number of P106S and TIPS plants were substantially limited (by ≤99%).

CONCLUSION

The ecological environment imposed by intense competition from a soybean crop sets a significant constraint for the landscape-level increase of both the E. indica single and double glyphosate resistance mutations in the agroecosystem and highlights the key role of crop competition in limiting the population growth of weeds, whether they are herbicide-resistant or susceptible. © 2022 Society of Chemical Industry.

A novel EPSPS Pro-106-His mutation confers the first case of glyphosate resistance in Digitaria sanguinalis

BACKGROUND

Digitaria sanguinalis has been identified as a species at high risk of evolving herbicide resistance, but thus far, there are no records of resistance to glyphosate. This weed is one of the most common weeds of summer crops in extensive cropping areas in Argentina. It shows an extended period of seedling emergence with several overlapping cohorts during spring and summer, and is commonly controlled with glyphosate. However, a D. sanguinalis population was implicated as a putative glyphosate-resistant biotype based on poor control at recommended glyphosate doses.

RESULTS

The field-collected D. sanguinalis population (Dgs R) from the Rolling Pampas has evolved glyphosate resistance. Differences in plant survival and shikimate levels after field-recommended and higher glyphosate doses were evident between Dgs R and the known susceptible (Dgs S) population; the resistance index was 5.1. No evidence of differential glyphosate absorption, translocation, metabolism or basal EPSPS activity was found between Dgs S and Dgs R populations; however, a novel EPSPS Pro-106-His point substitution is probably the primary glyphosate resistance-endowing mechanism. EPSPS in vitro enzymatic activity demonstrated that an 80-fold higher concentration of glyphosate is required in Dgs R to achieve similar EPSPS activity inhibition to that in the Dgs S population.

CONCLUSION

This study reports the first global case of glyphosate resistance in D. sanguinalis. This unlikely yet novel transversion at the second position of the EPSPS 106 codon demonstrates the intensity of glyphosate pressure in selecting unexpected glyphosate resistance alleles if they retain EPSPS functionality. © 2022 Society of Chemical Industry.

A dinitroaniline herbicide resistance mutation can be nearly lethal to plants

BACKGROUND

Lolium rigidum is the most important weed in Australian agriculture and pre-emergence dinitroaniline herbicides (e.g., trifluralin) are widely and persistently used for Lolium control. Consequently, evolution of resistance to dinitroaniline herbicides has been increasingly reported. Resistance-endowing target-site α-tubulin gene mutations are identified with varying frequency. This study investigated the putative fitness cost associated with the common resistance mutation Val-202-Phe and the rare resistance mutation Arg-243-Met causing helical plant growth.

RESULTS

Results showed a deleterious effect of Arg-243-Met on fitness when plants are homozygous for this mutation. This was evidenced as high plant mortality, severely diminished root and aboveground vegetative growth (lower relative growth rate), and very poor fecundity compared with the wild-type, which led to a nearly lethal fitness cost of >99.9% in competition with a wheat crop. A fitness penalty in vegetative growth was evident, but to a much lesser extent, in plants heterozygous for the Arg-243-Met mutation. By contrast, plants possessing the Val-202-Phe mutation exhibited a fitness advantage in vegetative and reproductive growth.

CONCLUSION

The α-tubulin mutations Arg-243-Met and Val-202-Phe have contrasting effects on fitness. These results help understand the absence of plants homozygous for the Arg-243-Met mutation and the high frequency of plants carrying the Val-202-Phe mutation in dinitroaniline-resistant L. rigidum populations. The α-tubulin Arg-243-Met mutation can have an exceptional fitness cost with nearly lethal effects on resistant L. rigidum plants. © 2022 Society of Chemical Industry.

Deciphering the Structure of Arabidopsis thaliana 5-enol-Pyruvyl-Shikimate-3-Phosphate Synthase: an Essential Step toward the Discovery of Novel Inhibitors to Supersede Glyphosate

Glyphosate interferes with plant aromatic metabolism through the inhibition of 5-enol-pyruvyl-shikimate-3-phosphate (EPSP) synthase [EPSPS, EC 2.5.1.19]. For this reason, EPSPS has been extensively studied in a vast array of organisms. This notwithstanding, up to date, the crystal structure of the protein has been solved exclusively in a few prokaryotes, while that of the plant enzyme has been only deduced in silico by similarity. This study aimed at determining the structure of EPSPS from the plant model species Arabidopsis thaliana, which has been cloned, heterologously expressed and affinity-purified. The kinetic properties of the enzyme have been determined, as well as its susceptibility to the inhibition brought about by glyphosate. The crystal structure of the protein has been resolved at high resolution (1.4 Å), showing open conformation of the enzyme, which is the state ready for substrate/inhibitor binding. This provides a framework for the structure-based design of novel EPSPS inhibitors. Surface regions near the active-site cleft entrance or at the interdomain hinge appear promising for inhibitor selectivity, while bound chloride near the active site is a potential placeholder for anionic moieties of future herbicides.

Vegetative and Fecundity Fitness Benefit Found in a Glyphosate-Resistant Eleusine indica Population Caused by 5-Enolpyruvylshikimate-3-Phosphate Synthase Overexpression

Fitness is an important trait in weed species that have developed herbicide resistance, including resistance to the popular herbicide glyphosate. Fitness cost is commonly found in weeds with glyphosate resistance, which is caused by target-site mutations. In this study, the vegetative and fecundity fitness traits in a glyphosate-resistant (GR) Eleusine indica population caused by 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) overexpression were investigated under glyphosate-free conditions. The results showed that the resistance index of the population resistant (R) to glyphosate compared with that of the population susceptible (WT) to it was approximately 4.0. Furthermore, EPSPS expression level in the R plants was 20.1-82.7 times higher than that in the WT plants. The dry weight of the R population was significantly higher than that of the WT population at the later growth stage after planting; a similar trend was observed for leaf area. In addition, seed production in the R population was 1.4 times higher than that in the WT population. The R and WT populations showed similar maximum germination rates and T₅₀ values. UPLC-MS/MS was performed for the metabolic extracts prepared from the leaves of R and WT populations to address changes in the metabolome. A total of 121 differential metabolites were identified between R and WT individuals. The levels of 6-hydroxy-1H-indole-3-acetamide and indole acetaldehyde, which are associated with auxin synthesis, were significantly higher in plants of the R population than in those of the WT population. However, some secondary metabolite levels were slightly lower in the R population than in the WT population. To conclude, in this study, vegetative and fecundity fitness benefits were found in the GR E. indica population. The results of metabolome analysis indicate that the increase in 6-hydroxy-1H-indole-3-acetamide and indole acetaldehyde levels may be the result of fitness benefit. Further studies should be conducted to confirm the functions of these metabolites.

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.

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.

Evolution of multiple target-site resistance mechanisms in individual plants of glyphosate-resistant Eleusine indica from China

BACKGROUND

Glyphosate has been used for weed control in South China in various situations for four decades, and most Eleusine indica populations are suspected to have evolved resistance to glyphosate. This research investigated underling target-site glyphosate resistance mechanisms in six field-collected, putative glyphosate-resistant (R) E. indica populations.

RESULTS

The six R E. indica populations were confirmed to be low (1.8 to 2.6-fold) to moderately (5.6- to 8.4-fold) resistant to glyphosate relative to the susceptible (S) population. Sixty-seven glyphosate-surviving plants from the six R populations were used to examine target-site resistance mechanisms. Target-site 5-enolpyruvylshikimate3-phosphate synthase (EPSPS) overexpression (OE) (plus further induction by glyphosate treatment) and gene copy number variation (CNV) occurred in 94% R plants, and among them, 16% had the P106A mutation and 49% had the heterozygous double TIPS (T102I + P106S) mutation (plus P381L). In addition, a low number of R plants (6%) only had the homologous TIPS (plus P381L) mutation. The (CT)6 insertion mutation in the EPSPS 5†-UTR always associates with EPSPS OE and CNV. Progeny plants possessing EPSPS OE/CNV (and P106A) displayed low level (up to 4.5-fold) glyphosate resistance. In contrast, plants homozygous for the TIPS mutation displayed higher (25-fold) resistance to glyphosate and followed by plants heterozygous for this mutation plus EPSPS OE/CNV (12-fold).

CONCLUSIONS

Target-site glyphosate resistance in E. indica populations from South China is common with prevalence of EPSPS OE/induction/CNV conferring low level resistance. Individual plants acquiring both the TIPS mutation and EPSPS OE/CNV are favored due to evolutionary advantages. The role of (CT)6 insertion mutation in EPSPS CNV is worth further investigation. © 2021 Society of Chemical Industry.

Development of non-transgenic glyphosate tolerant wheat by TILLING

Glyphosate (N-phosphonomethyl-glycine) is the world's most widely used broad spectrum, post-emergence herbicide. It inhibits the chloroplast-targeted enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), a component of the plant and microorganism-specific shikimate pathway and a key catalyst in the production of aromatic amino acids. Variants of EPSPS that are not inhibited by glyphosate due to particular amino acid alterations in the active site of the enzyme are known. Some of these variants have been identified in weed species that have developed resistance to glyphosate because of the strong selective pressure of continuous, heavy glyphosate use. We have used TILLING (Targeting Induced Local Lesions in Genomes), a non-transgenic, target-selected, reverse genetics, mutation breeding technique, and conventional genetic crosses, to identify and combine, through two rounds of mutagenesis, wheat lines having both T102I and P106S (so-called TIPS enzyme) mutations in both the A and the D sub-genome homoeologous copies of the wheat EPSPS gene. The combined effects of the T102I and P106S mutations are known from previous work in multiple species to minimize the binding of the herbicide while maintaining the affinity of the catalytic site for its native substrates. These novel wheat lines exhibit substantial tolerance to commercially relevant levels of glyphosate.

Marasmius oreades agglutinin enhances resistance of Arabidopsis against plant-parasitic nematodes and a herbivorous insect

BACKGROUND

Plant-parasitic nematodes and herbivorous insects have a significant negative impact on global crop production. A successful approach to protect crops from these pests is the in planta expression of nematotoxic or entomotoxic proteins such as crystal proteins from Bacillus thuringiensis (Bt) or plant lectins. However, the efficacy of this approach is threatened by emergence of resistance in nematode and insect populations to these proteins. To solve this problem, novel nematotoxic and entomotoxic proteins are needed. During the last two decades, several cytoplasmic lectins from mushrooms with nematicidal and insecticidal activity have been characterized. In this study, we tested the potential of Marasmius oreades agglutinin (MOA) to furnish Arabidopsis plants with resistance towards three economically important crop pests: the two plant-parasitic nematodes Heterodera schachtii and Meloidogyne incognita and the herbivorous diamondback moth Plutella xylostella.

RESULTS

The expression of MOA does not affect plant growth under axenic conditions which is an essential parameter in the engineering of genetically modified crops. The transgenic Arabidopsis lines showed nearly complete resistance to H. schachtii, in that the number of female and male nematodes per cm root was reduced by 86-91 % and 43-93 % compared to WT, respectively. M. incognita proved to be less susceptible to the MOA protein in that 18-25 % and 26-35 % less galls and nematode egg masses, respectively, were observed in the transgenic lines. Larvae of the herbivorous P. xylostella foraging on MOA-expression lines showed a lower relative mass gain (22-38 %) and survival rate (15-24 %) than those feeding on WT plants.

CONCLUSIONS

The results of our in planta experiments reveal a robust nematicidal and insecticidal activity of the fungal lectin MOA against important agricultural pests which may be exploited for crop protection.

Effect of EPSPS gene copy number and glyphosate selection on fitness of glyphosate-resistant Bassia scoparia in the field

The widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. With the continued use of glyphosate in GR sugar beet, the effect of increasing glyphosate rates (applied as single or sequential applications) on the fitness of GR B. scoparia individuals with variable EPSPS gene copies was tested under field conditions. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2214 g ae ha-1 or higher prevented seed production in B. scoparia plants with 2-4 (low levels of resistance) and 5-6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2-6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.

Characterization of glyphosate and quizalofop-p-ethyl multiple resistance in Eleusine indica

Glyphosate and Acetyl-coenzyme A Carboxylase (ACCase) inhibitors are popular herbicides that control goosegrass. However, some populations are difficult to control due to resistance resulting from the increasing selection pressure. The objectives of this research were to detect the multiple resistance levels, resistance mechanisms, and fitness costs of two goosegrass populations collected in China. The resistance indices of two resistant populations (denominated as R1 and R2) to glyphosate were 3.8 and 2.3, respectively; and it was 18.0 and 14.2 to quizalofop-p-ethyl, respectively. Shikimate accumulation in R1 and R2 populations was only 8% of that of the susceptible population after glyphosate treatment. A Pro-106-Ala mutation in EPSPS and an Asp-2078-Gly mutation in ACCase were present in both resistant populations. Both the expression level of EPSPS and ACCase in resistant populations were similar to that of susceptible populations. The leaf area of the individuals in wild-type populations was more than three times of the leaf area in the resistant populations. Similarly, resistant plants were 45-49% shorter, had 70-76% less fresh shoot weight, and 67-69% fewer seeds than wild-type plants. Goosegrass populations have evolved multiple resistance to glyphosate and the ACCase inhibitor quizalofop-p-ethyl in China. The Pro-106-Ala mutation in the EPSPS and the Asp-2078-Gly mutation in the ACCase were responsible for this resistance. In addition, a fitness cost exists in the resistant populations, and more work should conduct to clear which mutation is responsible for the fitness penalty.

Fitness Cost Associated With Enhanced EPSPS Gene Copy Number and Glyphosate Resistance in an Amaranthus tuberculatus Population

The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population of Amaranthus tuberculatus (common waterhemp), which has evolved resistance to glyphosate. The growth and fitness of seed families with contrasting levels of glyphosate resistance was assessed in the absence of glyphosate to determine their ability to compete for resources under intra- and interspecific competition. We identified a positive correlation between the level of glyphosate resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus identifying gene amplification as the mechanism of resistance within the population. Resistant A. tuberculatus plants were found to have a lower competitive response when compared to the susceptible phenotypes with 2.76 glyphosate resistant plants being required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.

Contrasting plant ecological benefits endowed by naturally occurring EPSPS resistance mutations under glyphosate selection

Concurrent natural evolution of glyphosate resistance single- and double-point EPSPS mutations in weed species provides an opportunity for the estimation of resistance fitness benefits and prediction of equilibrium resistance frequencies in environments under glyphosate selection. Assessment of glyphosate resistance benefit was conducted for the most commonly identified single Pro-106-Ser and less-frequent double TIPS mutations in the EPSPS gene evolved in the global damaging weed Eleusine indica. Under glyphosate selection at the field dose, plants with the single Pro-106-Ser mutation at homozygous state (P106S-rr) showed reduced survival and compromised vegetative growth and fecundity compared with TIPS plants. Whereas both homozygous (TIPS-RR) and compound heterozygous (TIPS-Rr) plants with the double TIPS resistance mutation displayed similar survival rates when exposed to glyphosate, a significantly higher fecundity in the currency of seed number was observed in TIPS-Rr than TIPS-RR plants. The highest plant fitness benefit was associated with the heterozygous TIPS-Rr mutation, whereas plants with the homozygous Pro-106-Ser and TIPS mutations exhibited, respectively, 31% and 39% of the fitness benefit revealed by the TIPS-Rr plants. Populations are predicted to reach stable allelic and genotypic frequencies after 20 years of glyphosate selection at which the WT allele is lost and the stable genotypic polymorphism is comprised by 2% of heterozygous TIPS-Rr, 52% of homozygous TIPS-RR and 46% of homozygous P106S-rr. The high inbreeding nature of E. indica is responsible for the expected frequency decrease in the fittest TIPS-Rr in favour of the homozygous TIPS-RR and P106S-rr. Mutated alleles associated with the glyphosate resistance EPSPS single EPSPS Pro-106-Ser and double TIPS mutations confer contrasting fitness benefits to E. indica under glyphosate treatment and therefore are expected to exhibit contrasting evolution rates in cropping systems under recurrent glyphosate selection.

Investigating the presence of compensatory evolution in dicamba resistant IAA16 mutated kochia (Bassia scoparia)†

BACKGROUND

Lack of fitness costs has been reported for multiple herbicide resistance traits, but the underlying evolutionary mechanisms are not well understood. Compensatory evolution that ameliorates resistance costs, has been documented in bacteria and insects but rarely studied in weeds. Dicamba resistant IAA16 (G73N) mutated kochia was previously found to have high fecundity in the absence of competition, regardless of significant vegetative growth defects. To understand if costs of dicamba resistance can be compensated through traits promoting reproductive success in kochia, we thoroughly characterized the reproductive growth and development of different G73N kochia biotypes. Flowering phenology, seed production and reproductive allocation were quantified through greenhouse studies, floral (stigma-anthers distance) and seed morphology, as well as resulting mating and seed dispersal systems were studied through time-course microcopy images.

RESULTS

G73N covaried with multiple phenological, morphological and ecological traits that improve reproductive fitness: (i) 16-60% higher reproductive allocation; (ii) longer reproduction phase through early flowering (2-7 days); (iii) smaller stigma-anthers separation (up to 60% reduction of herkogamy and dichogamy) that can potentially promote selfing and reproductive assurance; (iv) 'winged' seeds with 30-70% longer sepals that facilitate long-distance seed dispersal.

CONCLUSION

The current study demonstrates that costs of herbicide resistance can be ameliorated through coevolution of other fitness penalty alleviating traits. As illustrated in a hypothetical model, the evolution of herbicide resistance is an ongoing fitness maximization process, which poses challenges to contain the spread of resistance. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Evolution of Glyphosate-Resistant Weeds

Widespread adoption of glyphosate-resistant crops and concomitant reliance on glyphosate for weed control set an unprecedented stage for the evolution of herbicide-resistant weeds. There are now 48 weed species that have evolved glyphosate resistance. Diverse glyphosate-resistance mechanisms have evolved, including single, double, and triple amino acid substitutions in the target-site gene, duplication of the gene encoding the target site, and others that are rare or nonexistent for evolved resistance to other herbicides. This review summarizes these resistance mechanisms, discusses what is known about their evolution, and concludes with some of the impacts glyphosate-resistant weeds have had on weed management.

Comparative Transcriptome Analysis Revealing the Different Germination Process in Aryloxyphenoxypropionate-Resistant and APP-Susceptible Asia Minor Bluegrass (Polypogon fugax)

Herbicide-resistant mutations are predicted to exhibit fitness cost under herbicide-free conditions. Asia minor bluegrass (Polypogon fugax) is a common weed species in the winter crops. Our previous study established a P. fugax accession (LR) resistant to aryloxyphenoxypropionate (APP) herbicides, which also exhibited germination delay relative to the susceptible accession (LS). A comparative transcriptome was conducted to analyze the gene expression profile of LS and LR at two germination time points. A total of 11,856 and 23,123 differentially expressed genes (DEGs) were respectively identified in LS and LR. Most DEGs were involved in lipid metabolism, carbohydrate metabolism, amino acid metabolism, and secondary metabolites biosynthesis. Twenty-four genes involved in carbohydrate and fatty acid metabolism had higher relative expression levels in LS than LR during germination. Nine genes involved in gibberellin (GA) and abscisic acid (ABA) signal transduction showed different expression patterns in LS and LR, consistent with their different sensitivity to exogenous hormones treatments. This study first provided insight into transcriptional changes and interaction in the seed germination process of P. fugax. It compared the differential expression profile between APP herbicides resistance and susceptible accessions during germination, which contributed to understanding the association between herbicide resistance and fitness cost.

Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations

Since the initial report of glyphosate-resistant (GR) Amaranthus palmeri S. Watson in 2006, resistant populations have been reported in 28 states. The mechanism of resistance is amplification of a 399-kb extrachromosomal circular DNA, called the EPSPS replicon, and is unique to glyphosate-resistant plants. The replicon contains a single copy of the 10-kb 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene which causes the concomitant increased expression of EPSP synthase, the target enzyme of glyphosate. It is not known whether the resistance by this amplification mechanism evolved once and then spread across the country or evolved independently in several locations. To compare genomic representation and variation across the EPSPS replicon, whole genome shotgun sequencing (WGS) and mapping of sequences from both GR and susceptible (GS) biotypes to the replicon consensus sequence was performed. Sampling of GR biotypes from AZ, KS, GA, MD and DE and GS biotypes from AZ, KS and GA revealed complete contiguity and deep representation with sequences from GR plants, but lack of homogeneity and contiguity with breaks in coverage were observed with sequences from GS biotypes. The high sequence conservation among GR biotypes with very few polymorphisms which were widely distributed across the USA further supports the hypothesis that glyphosate resistance most likely originated from a single population. We show that the replicon from different populations was unique to GR plants and had similar levels of amplification.

Herbicides as anthropogenic drivers of eco-evo feedbacks in plant communities at the agro-ecological interface

Herbicides act as human-mediated novel selective agents and community disruptors, yet their full effects on eco-evolutionary dynamics in natural communities have only begun to be appreciated. Here, we synthesize how herbicide exposures can result in dramatic phenotypic and compositional shifts within communities at the agro-ecological interface and how these in turn affect species interactions and drive plant (and plant-associates') evolution in ways that can feedback to continue to affect the ecology and ecosystem functions of these assemblages. We advocate a holistic approach to understanding these dynamics that includes plastic changes and plant community transformations and also extends beyond this single trophic level targeted by herbicides to the effects on nontarget plant-associated organisms and their potential to evolve, thereby embracing the complexity of these real-world systems. We make explicit recommendations for future research to achieve this goal and specifically address impacts of ecology on evolution, evolution on ecology and their feedbacks so that we can gain a more predictive view of the fates of herbicide-impacted communities.

Mechanisms of Lolium rigidum multiple resistance to ALS- and ACCase-inhibiting herbicides and their impact on plant fitness

Three putative resistant (R1, R2, R3) and one susceptible (S) Lolium rigidum populations originating from Greece were studied for resistance to ALS and ACCase inhibiting herbicides, using whole plant, sequencing of als and accase gene, and in vitro ALS activity assays. The S and two R (R1, R2) populations were also evaluated for fitness in competition with wheat. The whole plant assay indicated unsatisfactory control of the R populations with mesosulfuron-methyl + iodosulfuron-methyl or pinoxaden application, whereas sequencing of the als gene revealed that all ALS-resistant individuals had a Pro-197 substitution by Leu, Glu, Ser, Ala, Thr, or Gln. In addition, the accase gene of all pinoxaden resistant individuals had an Ile-2041 substitution by Asn or Thr. Furthermore, sequencing of the individuals surviving mesosulfuron-methyl + iodosulfuron-methyl or pinoxaden treatment revealed co-existence of point mutations in the accase or als genes, respectively, demonstrating multiple resistance. The in vitro activity of the ALS enzyme confirmed that resistance to mesosulfuron-methyl + iodosulfuron-methyl was due altered target-site. The recorded higher vigor and greater competitive ability of S population against wheat as compared with that of the R populations suggests an associated fitness cost with multiple resistance.

A novel TIPT double mutation in EPSPS conferring glyphosate resistance in tetraploid Bidens subalternans

BACKGROUND

Bidens subalternans (greater beggarticks) is a tetraploid and troublesome weed infesting annual crops in most tropical regions of the world. A glyphosate-resistant (GR) B. subalternans biotype was detected in a soybean field from Paraguay. A series of physiological and molecular analyses were conducted to elucidate its resistance mechanisms.

RESULTS

The GR biotype had a high level of resistance (> 15-fold LD50 ), relative to a glyphosate-susceptible (GS) biotype. Shikimate accumulation was up to ten-fold greater for GS compared with GR. We found no differences in sensitivity when plants were treated and kept under lower (10/4 °C) or higher temperatures (25/20 °C). GS and GR had the same relative EPSPS gene copy number, and similar glyphosate absorption and translocation rates. Neither biotype metabolized glyphosate. A double amino acid substitution (TIPT - Thr102Ile and Pro106Thr) was found in only one EPSPS allele from one of the two EPSPS homoeologs present in tetraploid GR B. subalternans.

CONCLUSION

This is the first report of a TIPT double mutation conferring high levels of glyphosate resistance in a weed species. The presence of both wild-type and TIPT mutant EPSPS on the polyploid genome of GR B. subalternans may offset a potential fitness cost, requiring additional research to confirm the absence of deleterious effects. © 2019 Society of Chemical Industry.

No evidence for early fitness penalty in glyphosate-resistant biotypes of Conyza canadensis: Common garden experiments in the absence of glyphosate

Strong selection from herbicides has led to the rapid evolution of herbicide-resistant weeds, greatly complicating weed management efforts worldwide. In particular, overreliance on glyphosate, the active ingredient in RoundUp®, has spurred the evolution of resistance to this herbicide in ≥40 species. Previously, we reported that Conyza canadensis (horseweed) has evolved extreme resistance to glyphosate, surviving at 40× the original 1× effective dosage. Here, we tested for underlying fitness effects of glyphosate resistance to better understand whether resistance could persist indefinitely in this self-pollinating, annual weed. We sampled seeds from a single maternal plant ("biotype") at each of 26 horseweed populations in Iowa, representing nine susceptible biotypes (S), eight with low-level resistance (LR), and nine with extreme resistance (ER). In 2016 and 2017, we compared early growth rates and bolting dates of these biotypes in common garden experiments at two sites near Ames, Iowa. Nested ANOVAs showed that, as a group, ER biotypes attained similar or larger rosette size after 6 weeks compared to S or LR biotypes, which were similar to each other in size. Also, ER biotypes bolted 1-2 weeks earlier than S or LR biotypes. These fitness-related traits also varied among biotypes within the same resistance category, and time to bolting was inversely correlated with rosette size across all biotypes. Disease symptoms affected 40% of all plants in 2016 and 78% in 2017, so we did not attempt to measure lifetime fecundity. In both years, the frequency of disease symptoms was greatest in S biotypes and similar in LR versus ER biotypes. Overall, our findings indicate there are no early growth penalty and possibly no lifetime fitness penalty associated with glyphosate resistance, including extremely strong resistance. We conclude that glyphosate resistance is likely to persist in horseweed populations, with or without continued selection pressure from exposure to glyphosate.

Fitness of Herbicide-Resistant Weeds: Current Knowledge and Implications for Management

Herbicide resistance is the ultimate evidence of the extraordinary capacity of weeds to evolve under stressful conditions. Despite the extraordinary plant fitness advantage endowed by herbicide resistance mutations in agroecosystems under herbicide selection, resistance mutations are predicted to exhibit an adaptation cost (i.e., fitness cost), relative to the susceptible wild-type, in herbicide untreated conditions. Fitness costs associated with herbicide resistance mutations are not universal and their expression depends on the particular mutation, genetic background, dominance of the fitness cost, and environmental conditions. The detrimental effects of herbicide resistance mutations on plant fitness may arise as a direct impact on fitness-related traits and/or coevolution with changes in other life history traits that ultimately may lead to fitness costs under particular ecological conditions. This brings the idea that a “lower adaptive value” of herbicide resistance mutations represents an opportunity for the design of resistance management practices that could minimize the evolution of herbicide resistance. It is evident that the challenge for weed management practices aiming to control, minimize, or even reverse the frequency of resistance mutations in the agricultural landscape is to “create” those agroecological conditions that could expose, exploit, and exacerbate those life history and/or fitness traits affecting the evolution of herbicide resistance mutations. Ideally, resistance management should implement a wide range of cultural practices leading to environmentally mediated fitness costs associated with herbicide resistance 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.

Role of Glutamine Synthetase Isogenes and Herbicide Metabolism in the Mechanism of Resistance to Glufosinate in Lolium perenne L. spp. multiflorum Biotypes from Oregon

Glufosinate-resistant Lolium perenne L. spp. multiflorum biotypes from Oregon exhibited resistance levels up to 2.8-fold the field rate. One resistant biotype (MG) had an amino acid substitution in glutamine synthetase 2 (GS2), whereas the other (OR) exhibited the wild-type genotype. We hypothesized that the amino acid substitution in GS2 is involved in the resistance mechanism in MG and that non-target site resistance mechanisms are present in OR. OR metabolized glufosinate faster than the other two biotypes, with >75% of the herbicide metabolized in comparison to 50% in MG and the susceptible biotype. A mutation in GS2 co-segregating with resistance in MG did not reduce the enzyme activity, with results further supported by our enzyme homology models. This research supports the conclusion that a metabolism mechanism of glufosinate resistance is present in OR and that glufosinate resistance in MG is not due to an altered target site.