Target-site mutations conferring resistance to glyphosate in feathertop Rhodes grass (Chloris virgata) populations in Australia

Suppressive effects of increasing mungbean density on growth and reproduction of junglerice and feather fingergrass

Increased planting density can provide crops a competitive advantage over weeds. This study appraised the growth and seed production of two noxious grassy weeds, i.e. feather fingergrass (Chloris virgata SW.) and junglerice [Echinochloa colona (L.) Link] in response to different mungbean [Vigna radiata (L.) R. Wilczek] densities (0, 82, 164, 242, and 328 plants m-2). A target-neighbourhood study was conducted using a completely randomized design with five replications, and there were two experimental runs in 2016-2017. The leaf, stem, and total aboveground biomass of C. virgata was 86, 59, and 76% greater than E. colona. For seed production, E. colona outnumbered C. virgata by producing 74% more seeds. Mungbean density-mediated suppression of height was more pronounced for E. colona compared with C. virgata during the first 42 days. The presence of 164-328 mungbean plants m-2 reduced the number of leaves of E. colona and C. virgata by 53-72% and 52-57%, respectively. The reduction in the inflorescence number caused by the highest mungbean density was higher for C. virgata than E. colona. C. virgata and E. colona growing with mungbean produced 81 and 79% fewer seeds per plant. An increase in mungbean density from 82 to 328 plants m-2 reduced the total aboveground biomass of C. virgata and E. colona by 45-63% and 44-67%, respectively. Increased mungbean plant density can suppress weed growth and seed production. Although increased crop density contributes to better weed management, supplemental weed control will be needed.

CRISPR/Cas9-mediated homology donor repair base editing confers glyphosate resistance to rice (Oryza sativa L.)

Globally, CRISPR-Cas9-based genome editing has ushered in a novel era of crop advancements. Weeds pose serious a threat to rice crop productivity. Among the numerous herbicides, glyphosate [N-(phosphonomethyl)-glycine] has been employed as a post-emergent, broad-spectrum herbicide that represses the shikimate pathway via inhibition of EPSPS (5'-enolpyruvylshikimate-3-phosphate synthase) enzyme in chloroplasts. Here, we describe the development of glyphosate-resistant rice lines by site-specific amino acid substitutions (G172A, T173I, and P177S: GATIPS-mOsEPSPS) and modification of phosphoenolpyruvate-binding site in the native OsEPSPS gene employing fragment knockout and knock-in of homology donor repair (HDR) template harboring desired mutations through CRISPR-Cas9-based genome editing. The indigenously designed two-sgRNA OsEPSPS-NICTK-1_pCRISPR-Cas9 construct harboring rice codon-optimized SpCas9 along with OsEPSPS-HDR template was transformed into rice. Stable homozygous T₂ edited rice lines revealed significantly high degree of glyphosate-resistance both in vitro (4 mM/L) and field conditions (6 ml/L; Roundup Ready) in contrast to wild type (WT). Edited T₂ rice lines (ER_1-6) with enhanced glyphosate resistance revealed lower levels of endogenous shikimate (14.5-fold) in contrast to treated WT but quite similar to WT. ER_1-6 lines exhibited increased aromatic amino acid contents (Phe, two-fold; Trp, 2.5-fold; and Tyr, two-fold) than WT. Interestingly, glyphosate-resistant Cas9-free EL_1-6 rice lines displayed a significant increment in grain yield (20%-22%) in comparison to WT. Together, results highlighted that the efficacy of GATIPS mutations in OsEPSPS has tremendously contributed in glyphosate resistance (foliar spray of 6 ml/L), enhanced aromatic amino acids, and improved grain yields in rice. These results ensure a novel strategy for weed management without yield penalties, with a higher probability of commercial release.

Glyphosate Efficacy in Chloris virgata Sw. in Response to Temperature and Tank Mixing

Glyphosate alone or a tank mixture of glyphosate and 2,4-D is commonly used for broad-spectrum weed control under fallow conditions in Australia. Air temperature or mixing glyphosate with 2,4-D, may influence the efficacy of glyphosate on feather fingergrass (Chloris virgata Sw.), a problematic summer-season weed of Australia. Dose-response studies were conducted with four populations of feather fingergrass under temperature-controlled glasshouse conditions (35/25 °C and 25/15 °C at 12 h/12 h) to assess the level of glyphosate resistance in relation to temperature regimes. Four parameter log-logistic models were used to develop dose-response curves. Based on plant mortality percentage, LD₅₀ (lethal dose for 50% mortality) values of glyphosate at 25/15 °C for populations Ch, SGM2, SGW2, and CP2 were 137, 60, 650, and 1067 g ae ha^-1, respectively. However, at 35/25 °C, the corresponding LD₅₀ values were 209, 557, 2108, and 2554 g ae ha^-1, respectively. A similar response was observed for the parameter GR₅₀ (dose for 50% growth reduction) values of glyphosate. These results indicate that populations SGW2 and CP2 are highly glyphosate-resistant and in the summer season, it may be very difficult to control these populations due to poor glyphosate efficacy. These results further suggest that the efficacy of glyphosate for feather fingergrass control can be improved if applied during cooler temperatures (25/15 °C) or the spring season compared with warmer temperatures (35/25 °C) or the summer season. In another study, 2,4-D antagonized glyphosate remarkably in the CP2 (glyphosate-resistant) population but only marginally in the Ch (glyphosate-susceptible) population. Thus, it is not advisable to mix 2,4-D with glyphosate for the control of glyphosate-resistant feather fingergrass populations. The results further suggest that the use of this mixture is useful if the feather fingergrass is not glyphosate-resistant; however, the use of the mixture is to be avoided if the population is glyphosate-resistant in order to not exacerbate the potential resistance problem.

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.

Multiple evolutionary origins of glyphosate resistance in Lolium multiflorum

The multitude of herbicide resistance patterns that have evolved in different weed species is a remarkable example of the rapid adaptation to anthropogenic‐driven disturbance. Recently, resistance to glyphosate was identified in multiple populations of Lolium multiflorum in Oregon. We used phenotypic approaches, as well as population genomic and gene expression analyses, to determine whether known mechanisms were responsible for glyphosate resistance and whether resistance phenotypes evolved independently in different populations, and to identify potential loci contributing to resistance. We found no evidence of genetic alterations or expression changes at known target and non‐target‐site resistance mechanisms of glyphosate. Population genomic analyses indicated that resistant populations tended to have largely distinct ancestry from one another, suggesting that glyphosate resistance did not spread among populations by gene flow. Rather, resistance appears to have evolved independently on different genetic backgrounds. We also detected potential loci associated with the resistance phenotype, some of which encode proteins with potential effects on herbicide metabolism. Our results suggest that Oregon populations of L. multiflorum evolved resistance to glyphosate due to a novel mechanism. Future studies that characterize the gene or genes involved in resistance will be necessary to confirm this conclusion.

Glyphosate resistance in Chloris radiata from colombian rice fields involves one target-site mechanism

At present, appearance of herbicide resistant weeds is not new because repeated herbicide treatments per agricultural year/cycle are usual in both perennial and annual crops worldwide. Characterizing resistance mechanisms implied in each herbicide resistant weed is the best tool and the basis to develop integrated weed management (IWM) strategies. The main resistance mechanisms which confer low sensibility to glyphosate in a previously confirmed glyphosate-resistant Chloris radiata population (ChrR), occurring in Colombian rice fields, were characterized. Pure line selection by clone plants showed high resistance levels in ChrR. Comparing with GR50 and LD50 values, ChrR was 9.6 and 10.8 times more resistant with respect to a representative susceptible population (ChrS). The nontarget site mechanisms reduced glyphosate absorption and translocation did not contribute to the glyphosate resistance of the ChrR population. However, enzyme activity assays and DNA sequencing demonstrated that at least one target-site resistance mechanism is involved in such resistance. All ten ChrR plants tested had the amino acid substitution Pro-106-Ser. The results may be crucial to decrease the resistance distribution of C. radiata in Colombia by implementing IWM programs. The change in weed control strategies in rice fields from Colombia must include herbicides with different mode of action from glyphosate and non chemical methods to preserve the useful life of glyphosate longer for weed control in the country.

Evaluation of Preemergent Herbicides for Chloris virgata Control in Mungbean

Chloris virgata is a problematic weed in mungbean crops due to its high seed production, resistance to glyphosate and high dispersal ability. Pot and field experiments were conducted in 2020 and 2021 to evaluate a range of preemergent (PRE) herbicides for C. virgata control in mungbean. In the field and pot studies, isoxaflutole 75 g ai ha^-1 caused crop injury, and in the field experiment, it reduced mungbean yield by 61% compared with the best treatment (pyroxasulfone 100 g ai ha^-1). In the field and pot experiments, dimethenamid-P 720 g ai ha^-1, pyroxasulfone 100 g ai ha^-1 and S-metolachlor 1400 g ai ha^-1 provided >88% control of C. virgata (for reduced biomass) and in the field experiment, these herbicides resulted in improved yield by 230%, 270% and 170%, respectively, compared with nontreated control (250 kg ha^-1). Similarly, pendimethalin 1000 g ai ha^-1 and trifluralin 600 g ai ha^-1 provided >89% control (biomass) of C. virgata, and in the field experiment, these resulted in improved yields of 230% and 160%, respectively, compared with the nontreated control. PRE herbicides such as diuron 750 g ai ha^-1, linuron 1100 g ai ha^-1, metribuzin 360 g ha^-1, terbuthylazine 750 g ai ha^-1, imazapic 48 g ai ha^-1 and imazethapyr 70 g ha^-1 although did not cause crop injury; however, these herbicides did not control C. virgata. Flumioxazin 90 g ai ha^-1 caused reduced biomass of C. virgata by 80% compared with the nontreated control, and in the field experiment, it resulted in improved yield by 140% compared with the nontreated control. This study suggests the potential use of herbicides, such as dimethenamid-P, pyroxasulfone and S-metolachlor in addition to pendimethalin and trifluralin, for C. virgata control in mungbean. Further studies are needed to determine the efficacy of dimethenamid-P, S-metolachlor and pyroxasulfone for controlling other troublesome weeds in mungbean.

Transcriptome Analysis of Chloris virgata, Which Shows the Fastest Germination and Growth in the Major Mongolian Grassland Plant

Plants in Mongolian grasslands are exposed to short, dry summers and long, cold winters. These plants should be prepared for fast germination and growth activity in response to the limited summer rainfall. The wild plant species adapted to the Mongolian grassland environment may allow us to explore useful genes, as a source of unique genetic codes for crop improvement. Here, we identified the Chloris virgata Dornogovi accession as the fastest germinating plant in major Mongolian grassland plants. It germinated just 5 h after treatment for germination initiation and showed rapid growth, especially in its early and young development stages. This indicates its high growth potential compared to grass crops such as rice and wheat. By assessing growth recovery after animal bite treatment (mimicked by cutting the leaves with scissors), we found that C. virgata could rapidly regenerate leaves after being damaged, suggesting high regeneration potential against grazing. To analyze the regulatory mechanism involved in the high growth potential of C. virgata, we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis, respectively. The best-aligned sequences were annotated with gene ontology groups. When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata. Plant development is tightly regulated by phytohormones such as brassinosteroids, gibberellic acid, abscisic acid, and strigolactones. Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. We discuss the possibility that C. virgata phytohormone signaling and biosynthesis genes regulate early germination and growth advantages. Comprehensive transcriptome information will provide a useful resource for gene discovery and facilitate a deeper understanding of the diversity of the regulatory systems that have evolved in C. virgata while adapting to severe environmental conditions.

Endosidin20-1 is more potent than endosidin20 in inhibiting plant cellulose biosynthesis and molecular docking analysis of cellulose biosynthesis inhibitors on modeled cellulose synthase structure

Endosidin20 (ES20) is a recently identified cellulose biosynthesis inhibitor (CBI) that targets the catalytic site of plant cellulose synthase (CESA). Here, we screened over 600 ES20 analogs and identified nine active analogs named ES20-1 to ES20-9. Among these, endosidin20-1 (ES20-1) had stronger inhibitory effects on plant growth and cellulose biosynthesis than ES20. At the biochemical level, we demonstrated that ES20-1, like ES20, directly interacts with CESA6. At the cellular level, this molecule, like ES20, induced the accumulation of cellulose synthase complexes at the Golgi apparatus and inhibited their secretion to the plasma membrane. Like ES20, ES20-1 likely targets the catalytic site of CESA. However, through molecular docking analysis using a modeled structure of full-length CESA6, we found that both ES20 and ES20-1 might have another target site at the transmembrane regions of CESA6. Besides ES20, other CBIs such as isoxaben, C17, and flupoxam are widely used tools to dissect the mechanism of cellulose biosynthesis and are also valuable resources for the development of herbicides. Here, based on mutant genetic analysis and molecular docking analysis, we have identified the potential target sites of these CBIs on a modeled CESA structure. Some bacteria also produce cellulose, and both ES20 and ES20-1 inhibited bacterial cellulose biosynthesis. Therefore, we conclude that ES20-1 is a more potent analog of ES20 that inhibits intrinsic cellulose biosynthesis in plants, and both ES20 and ES20-1 show an inhibitory effect on bacterial growth and cellulose synthesis, making them excellent tools for exploring the mechanisms of cellulose biosynthesis across kingdoms.

Confirmation of Multiple Resistant Chloris radiata Population, Harvested in Colombian Rice Fields

This paper reports the first C. radiata population with resistance to glyphosate and multiple resistance to the acetolactate synthase (ALS) inhibitor, imazamox. Two populations, one putative resistant (R) and one susceptible (S), were used in the studies. Dose–response experiments were performed to evaluate the resistance factor (RF). Shikimic acid accumulation, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) and ALS enzyme activities were studied together with chemical integrated weed management (adjuvants and alternative herbicides). The resistance to glyphosate and imazamox was confirmed based on the dry weight reduction, visual evaluation and survival. The results of dose–response curve assays showed for the R population intermedium RF for glyphosate (5.1 and 9.7 for amount of herbicide needed to reduce the dry weight by 50% GR50 and lethal dose of 50% LD50, respectively) and high RF for imazamox (34.9 and 37.4, respectively). The low shikimic acid accumulation in R population confirmed the glyphosate resistance. The glyphosate concentration which inhibited the EPSPS enzyme in 50% (I50) was approximately 20 times higher for R population than the S population, while the imazamox I50 in ALS enzyme for the R plants was 89 times greater than the S plants. In the chemical integrated weed management, the foliar retention and effectivity assays showed that the use of adjuvants improves the retention of glyphosate and imazamox, and the reduction in dry weight of weeds. The alternative herbicides study showed that the acetyl-CoA carboxylase (ACCase) inhibitors, paraquat and glufosinate, had better results for control in this species. However, poor control was observed with bispyribac-sodium, metsulfuron-methyl and quinclorac, indicating possible cross-resistance for ALS-inhibitors and also multiple resistance for auxinic herbicides (quinclorac). Nevertheless dose–response experiments are required to confirm this assumption.

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.

History and Outlook for Glyphosate-Resistant Crops

Glyphosate-resistant (GR) crops, commercially referred to as glyphosate-tolerant (GT), started the revolution in crop biotechnology in 1996. Growers rapidly accepted GR crops whenever they became available and made them the most rapidly adopted technology in agriculture history. Adoption usually meant sole reliance on glyphosate [N-(phosphonomethyl)glycine, CAS No. 1071-83-6] for weed control. Not surprisingly, weeds eventually evolved resistance and are forcing growers to change their weed management practices. Today, the widespread dissemination of GR weeds that are also resistant to other herbicide modes-of-action (MoA) has greatly reduced the value of the GR crop weed management systems. However, growers continue to use the technology widely in six major crops throughout North and South America. Integrated chemistry and seed providers seek to sustain glyphosate efficacy by promoting glyphosate combinations with other herbicides and stacking the traits necessary to enable the use of partner herbicides. These include glufosinate {4-[hydroxy(methyl)phosphinoyl]-DL-homoalanine, CAS No. 51276-47-2}, dicamba (3,6-dichloro-2-methoxybenzoic acid, CAS No. 1918-00-9), 2,4-D [2-(2,4-dichlorophenoxy)acetic acid, CAS No. 94-75-7], 4-hydroxyphenyl pyruvate dioxygenase inhibitors, acetyl coenzyme A carboxylase (ACCase) inhibitors, and other herbicides. Unfortunately, herbicide companies have not commercialized a new MoA for over 30 years and have nearly exhausted the useful herbicide trait possibilities. Today, glyphosate-based crop systems are still mainstays of weed management, but they cannot keep up with the capacity of weeds to evolve resistance. Growers desperately need new technologies, but no technology with the impact of glyphosate and GR crops is on the horizon. Although the expansion of GR crop traits is possible into new geographic areas and crops such as wheat and sugarcane and could have high value, the Roundup Ready® revolution is over. Its future is at a nexus and dependent on a variety of issues.

Target-Site Resistance to Glyphosate in Chloris Virgata Biotypes and Alternative Herbicide Options for its Control

Due to the overdependence on glyphosate to manage weeds in fallow conditions, glyphosate resistance has developed in various biotypes of several grass weeds, including Chloris virgata Sw. The first case of glyphosate resistance in C. virgata was found in 2015 in Australia, and since then several cases have been confirmed in several biotypes across Australia. Pot studies were conducted with 10 biotypes of C. virgata to determine glyphosate resistance levels. The biotypes were identified as either susceptible, moderately resistant or highly resistant based on the glyphosate dose required to kill 50% of plants. Two glyphosate-susceptible (GS) and two glyphosate-resistant (GR) biotypes were identified by the dose-response study and analyzed for the presence of target-site mutation in the 5–enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. Performance of alternative herbicides to glyphosate as well as the double-knock herbicide approach was evaluated on the two GS (Ch and SGM2) and two GR (SGW2 and CP2) biotypes. Three herbicides, clethodim, haloxyfop and paraquat, were found to be effective (100% control) against all four biotypes when applied at the 4–5 leaf stage. All the sequential herbicide treatments, such as glyphosate followed by paraquat and glufosinate-ammonium followed by paraquat, provided 100% control of all four biotypes of C. virgata. This study identified effective herbicide options for the control of GR C. virgata and showed that target-site mutations were involved in the resistance of two biotypes to glyphosate (SGW2 and CP2). Results could aid farmers in selecting herbicides to manage C. virgata in their fields.

Resistance Evolution to EPSPS Inhibiting Herbicides in False Barley (Hordeum murinum) Harvested in Southern Spain

A failure of the EPSPS-inhibiting herbicide glyphosate to control several populations of Hordeum murinum subsp. leporinum (or H. murinum) occurred in southern Spain after more than fifteen applications in both crop (olive, orchards, and citrus) and non-crop (dry areas, roadsides and ditches) areas. Eight out of 18 populations studied were resistant (R) to glyphosate with R factors higher than four based on GR50. These populations also had the highest values of LD50 and the lowest levels of shikimic acid accumulation. Two adjuvants tested increased glyphosate efficacy in both susceptible (S) and R populations thanks to better spray foliar retention. Moreover, PS I-, PS II-, and ACCase-inhibiting herbicides, in pre- or post-emergence, proved to be the best chemical alternatives with different sites of action (SoA) to control both S and glyphosate-R populations. This study represents the first report worldwide of glyphosate resistance in H. murinum found in very different crop and non-crop areas from southern Spain. To design chemical strategies to implement integrated weed management programs for glyphosate-R H. murinum, both adjuvants and herbicides with alternative SoA as well as application timings should be considered.

Target-site EPSPS Pro-106-Ser mutation in Conyza canadensis biotypes with extreme resistance to glyphosate in Ohio and Iowa, USA

Documenting the diversity of mechanisms for herbicide resistance in agricultural weeds is helpful for understanding evolutionary processes that contribute to weed management problems. More than 40 species have evolved resistance to glyphosate, and at least 13 species have a target-site mutation at position 106 of EPSPS. In horseweed (Conyza canadensis), this p106 mutation has only been reported in Canada. Here, we sampled seeds from one plant (= biotype) at 24 sites in Ohio and 20 in Iowa, screened these biotypes for levels of resistance, and sequenced their DNA to detect the p106 mutation. Resistance categories were based on 80% survival at five glyphosate doses: S (0×), R1 (1×), R2 (8×), R3 (20×), or R4 (40×). The p106 mutation was not found in the19 biotypes scored as S, R1, or R2, while all 25 biotypes scored as R3 or R4 had the same proline-to-serine substitution at p106. These findings represent the first documented case of target-site mediated glyphosate resistance in horseweed in the United States, and the first to show that this mutation was associated with very strong resistance. We hypothesize that the p106 mutation has occurred multiple times in horseweed and may be spreading rapidly, further complicating weed management efforts.

New Case of False-Star-Grass (Chloris distichophylla) Population Evolving Glyphosate Resistance

Chloris distichophylla, suspected of glyphosate resistance (GR), was collected from areas of soybean cultivation in Rio Grande do Sul, Brazil. A comparison was made with a susceptible population (GS) to evaluate the resistance level, mechanisms involved, and control alternatives. Glyphosate doses required to reduce the dry weight (GR50) or cause a mortality rate of 50% (LD50) were around 5.1–3 times greater in the GR population than in the GS population. The shikimic acid accumulation was around 6.2-fold greater in GS plants than in GR plants. No metabolized glyphosate was found in either GR or GS plants. Both populations did not differ in the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) basal activity or in vitro inhibition of EPSPS activity by glyphosate (I50). The maximum glyphosate absorption was observed at 96 hours after treatment (HAT), which was twofold higher in the GS plants than in the GR plants. This confirms the first case of glyphosate resistance in C. distichophylla. In addition, at 96 HAT, the GS plants translocated more 14C-glyphosate than the GR ones. The best options for the chemical control of both C. distichophylla populations were clethodim, quizalofop, paraquat, glufosinate, tembotrione, diuron, and atrazine. The first case of glyphosate resistance in C. distichophylla was due to impaired uptake and translocation. Chemical control using multiple herbicides with different modes of action (MOA) could be a tool used for integrated weed management (IWM) programs.

Physiological and molecular analysis of glyphosate resistance in non-rapid response Ambrosia trifida from Wisconsin

BACKGROUND

We previously identified a glyphosate-resistant A. trifida phenotype from Wisconsin USA that showed a non-rapid response to glyphosate. The mechanism of glyphosate resistance in this phenotype has yet to be elucidated. We conducted experiments to investigate non-target-site resistance and target-site resistance mechanisms. The roles of glyphosate absorption, translocation, and metabolism in resistance of this phenotype have not been reported previously, nor have EPSPS protein abundance or mutations to the full-length sequence of EPSPS.

RESULTS

Whole-plant dose-response results confirmed a 6.5-level of glyphosate resistance for the resistant (R) phenotype compared to a susceptible (S) phenotype. Absorption and translocation of 14 C-glyphosate were similar between R and S phenotypes over 72 h. Glyphosate and AMPA concentrations in leaf tissue did not differ between R and S phenotypes over 96 h. In vivo shikimate leaf disc assays confirmed that glyphosate EC50 values were 4.6- to 5.4-fold greater for the R than S phenotype. Shikimate accumulation was similar between phenotypes at high glyphosate concentrations (>1000 μM), suggesting that glyphosate entered chloroplasts and inhibited EPSPS. This finding was supported by results showing that EPSPS copy number and EPSPS protein abundance did not differ between R and S phenotypes, nor did EPSPS sequence at Gly101, Thr102, and Pro106 positions. Comparison of full-length EPSPS sequences found five nonsynonymous polymorphisms that differed between R and S phenotypes. However, their locations were distant from the glyphosate target site and, therefore, not likely to affect enzyme-glyphosate interaction.

CONCLUSION

The results suggest that a novel mechanism confers glyphosate resistance in this A. trifida phenotype. © 2019 Society of Chemical Industry.

Evolution of Target-Site Resistance to Glyphosate in an Amaranthus palmeri Population from Argentina and Its Expression at Different Plant Growth Temperatures

The mechanism and expression of resistance to glyphosate at different plant growing temperatures was investigated in an Amaranthus palmeri population (VM1) from a soybean field in Vicuña Mackenna, Cordoba, Argentina. Resistance was not due to reduced glyphosate translocation to the meristem or to EPSPS duplication, as reported for most US samples. In contrast, a proline 106 to serine target-site mutation acting additively with EPSPS over-expression (1.8-fold increase) was respectively a major and minor contributor to glyphosate resistance in VM1. Resistance indices based on LD₅₀ values generated using progenies from a cross between 52 PS106 VM1 individuals were estimated at 7.1 for homozygous SS106 and 4.3 for heterozygous PS106 compared with homozygous wild PP106 plants grown at a medium temperature of 24 °C day/18 °C night. A larger proportion of wild and mutant progenies survived a single commonly employed glyphosate rate when maintained at 30 °C day/26 °C night compared with 20 °C day/16 night in a subsequent experiment. Interestingly, the P106S mutation was not identified in any of the 920 plants analysed from 115 US populations, thereby potentially reflecting the difference in A. palmeri control practices in Argentina and USA.

Response of Chloris truncata to moisture stress, elevated carbon dioxide and herbicide application

Herbicide resistance has been observed in Chloris truncata, an Australian native C4 grass and a summer-fallow weed, which is common in no-till agriculture situations where herbicides are involved in crop management. To investigate the role of drought and increased atmospheric carbon dioxide (CO2) in determining weed growth, three trials were conducted using a 'glyphosate-resistant' and a 'glyphosate-susceptible' biotype. The first two trials tested the effect of herbicide (glyphosate) application on plant survival and growth under moisture stress and elevated CO2 respectively. A third trial investigated the effect on plant growth and reproduction under conditions of moisture stress and elevated CO2 in the absence of herbicide. In the first trial, water was withheld from half of the plants prior to application of glyphosate to all plants, and in the second trial plants were grown in either ambient (450 ppm) or elevated CO2 levels (750 ppm) prior to, and following, herbicide application. In both biotypes, herbicide effectiveness was reduced when plants were subjected to moisture stress or if grown in elevated CO2. Plant productivity, as measured by dry biomass per plant, was reduced with moisture stress, but increased with elevated CO2. In the third trial, growth rate, biomass and seed production were higher in the susceptible biotype compared to the resistant biotype. This suggests that a superior ability to resist herbicides may come at a cost to overall plant fitness. The results indicate that control of this weed may become difficult in the future as climatic conditions change.

EPSPS duplication and mutation involved in glyphosate resistance in the allotetraploid weed species Poa annua L

BACKGROUND

Poa annua is a widespread winter annual weed species in California. Recently, poor control of this species with glyphosate was reported by growers in an almond orchard in California with a history of repetitive glyphosate use. The objectives of this research were to evaluate the level of glyphosate resistance in a developed S4 P. annua line (R) and identify the mechanisms of resistance involved.

RESULTS

Whole-plant dose-response experiments confirmed glyphosate resistance in R, which required 18-fold more glyphosate to achieve a 50% growth reduction compared with a susceptible line (S), results that were supported by the lower shikimate accumulation observed in R compared with S. No differences in glyphosate absorption, translocation, or metabolism were observed, suggesting that non-target-site mechanisms of resistance are not involved in the resistance phenotype. A missense single nucleotide polymorphism was observed in EPSPS coding position 106 in R, resulting in a leucine to proline substitution. This polymorphism was observed exclusively in P. supina EPSPS homeologs. A seven-fold increase in the number of copies of EPSPS alleles was observed in R compared with S.

CONCLUSIONS

We report the first case of glyphosate resistance associated with both EPSPS duplication and target-site mutation at position 106, leading to high levels of glyphosate resistance in the allotetraploid weed species Poa annua L. Data obtained in this research will be useful for the development of diagnostic tools for rapid glyphosate resistance identification, monitoring and containment. © 2018 Society of Chemical Industry.

Molecular basis of natural tolerance to glyphosate in Convolvulus arvensis

Convolvulus arvensis is a troublesome weed that is naturally tolerant to glyphosate. This weed tolerates glyphosate at a rate 5.1 times higher than that of glyphosate-susceptible Calystegia hederacea. Glyphosate-treated C. arvensis plants accumulated less shikimic acid than C. hederacea plants. The overexpression of EPSPS genes from the two species in transgenic Arabidopsis thaliana resulted in similar glyphosate tolerance levels. qPCR of genomic DNA revealed that the EPSPS copy number in C. arvensis was approximately 2 times higher than that in C. hederacea. Moreover, glyphosate treatment caused a marked increase in EPSPS mRNA in C. arvensis compared to C. hederacea. GUS activity analysis showed that the promoter of CaEPSPS (CaEPSPS-P) highly improved GUS expression after glyphosate treatment, while no obvious differential GUS expression was observed in ChEPSPS-P transgenic A. thaliana in the presence or absence of glyphosate. Based on the obtained results, two coexisting mechanisms may explain the natural glyphosate tolerance in C. arvensis: (i) high EPSPS copy number and (ii) specific promoter-mediated overexpression of EPSPS after glyphosate treatment.

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.

Desensitizing plant EPSP synthase to glyphosate: Optimized global sequence context accommodates a glycine-to-alanine change in the active site

5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the transfer of a carboxyvinyl group from phosphoenolpyruvate (PEP) to shikimate-3-phosphate and in plants is the target of the herbicide glyphosate. EPSPSs with high catalytic efficiency and insensitivity to glyphosate are of microbial origin, including the enzyme from Agrobacterium strain CP4, in which insensitivity is conferred by an active site alanine. In the sequence context of plant EPSPSs, alanine in place of glycine at the equivalent position interferes with the binding of both glyphosate and PEP. We show here that iterative optimization of maize EPSPS containing the G101A substitution yielded variants on par with CP4 in terms of catalytic activity in the presence of glyphosate. The improvement relative to G101A alone was entirely due to reduction in Km for PEP from 333 to 18 μm, versus 9.5 μm for native maize EPSPS. A large portion of the reduction in Km was conferred by two down-sizing substitutions (L97C and V332A) within 8 Å of glyphosate, which together reduced Km for PEP to 43 μm Although the original optimization was conducted with maize EPSPS, contextually homologous substitutions conferred similar properties to the EPSPSs of other crops. We also discovered a variant having the known glyphosate-desensitizing substitution P106L plus three additional ones that reduced the Km for PEP from 47 μm, observed with P106L alone, to 10.3 μm The improvements obtained with both Ala101 and Leu106 have implications regarding glyphosate-tolerant crops and weeds.

Overview of glyphosate-resistant weeds worldwide

Glyphosate is the most widely used and successful herbicide discovered to date, but its utility is now threatened by the occurrence of several glyphosate-resistant weed species. Glyphosate resistance first appeared in Lolium rigidum in an apple orchard in Australia in 1996, ironically the year that the first glyphosate-resistant crop (soybean) was introduced in the USA. Thirty-eight weed species have now evolved resistance to glyphosate, distributed across 37 countries and in 34 different crops and six non-crop situations. Although glyphosate-resistant weeds have been identified in orchards, vineyards, plantations, cereals, fallow and non-crop situations, it is the glyphosate-resistant weeds in glyphosate-resistant crop systems that dominate the area infested and growing economic impact. Glyphosate-resistant weeds present the greatest threat to sustained weed control in major agronomic crops because this herbicide is used to control weeds with resistance to herbicides with other sites of action, and no new herbicide sites of action have been introduced for over 30 years. Industry has responded by developing herbicide resistance traits in major crops that allow existing herbicides to be used in a new way. However, over reliance on these traits will result in multiple-resistance in weeds. Weed control in major crops is at a precarious point, where we must maintain the utility of the herbicides we have until we can transition to new weed management technologies. © 2017 Society of Chemical Industry.

Evaluation of glyphosate resistance in Arabidopsis thaliana expressing an altered target site EPSPS

BACKGROUND

Glyphosate-resistant goosegrass has recently evolved and is homozygous for the double mutant of EPSPS (T102 I, P106 S or TIPS). These same mutations combined with EPSPS overexpression, have been used to create transgenic glyphosate-resistant crops. Arabidopsis thaliana (Wt EPSPS Ki ∼ 0.5 μM) was engineered to express a variant AtEPSPS-T102 I, P106 A (TIPA Ki = 150 μM) to determine the resistance magnitude for a more potent variant EPSPS that might evolve in weeds.

RESULTS

Transgenic A. thaliana plants, homozygous for one, two or four copies of AtEPSPS-TIPA, had resistance (IC50 values, R/S) as measured by seed production ranging from 4.3- to 16-fold. Plants treated in reproductive stage were male sterile with a range of R/S from 10.1- to 40.6-fold. A significant hormesis (∼ 63% gain in fresh weight) was observed for all genotypes when treated at the initiation of reproductive stage with 0.013 kg ha-1 . AtEPSPS-TIPA enzyme activity was proportional to copy number and correlated with resistance magnitude.

CONCLUSIONS

A. thaliana, as a model weed expressing one copy of AtEPSPS-TIPA (300-fold more resistant), had only 4.3-fold resistance to glyphosate for seed production. Resistance behaved as a single dominant allele. Vegetative tissue resistance was 4.7-fold greater than reproductive tissue resistance and was linear with gene copy number. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Pro-106-Ser mutation and EPSPS overexpression acting together simultaneously in glyphosate-resistant goosegrass (Eleusine indica)

Glyphosate has been used for more than 15 years for weed management in citrus groves in the Gulf of Mexico, at up to 3-4 applications per year. Goosegrass (Eleusine indica (L.) Gaertn.) control has sometimes failed. In this research, the mechanisms governing three goosegrass biotypes (Ein-Or from an orange grove, and Ein-Pl1 and Ein-Pl2 from Persian lime groves) with suspected resistance to glyphosate were characterized and compared to a susceptible biotype (Ein-S). Dose-response and shikimate accumulation assays confirmed resistance of the resistant (R) biotypes. There were no differences in glyphosate absorption, but the R biotypes retained up to 62-78% of the herbicide in the treated leaf at 96 h after treatment (HAT), in comparison to the Ein-S biotype (36%). The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity in the Ein-Or and Ein-S biotypes was over 100-fold lower than the Ein-Pl1 and Ein-Pl2 ones. The latter showed a high EPSPS-basal activity, a mutation at Pro-106-Ser position in the EPSPS gene, and EPSPS overexpression. The EPSPS basal and EPSPS overexpression were positively correlated. The R goosegrass biotypes displayed poor glyphosate translocation. Furthermore, this grassweed showed, for the first time, two mechanisms at the target-site level (Pro-106-Ser mutation + EPSPS overexpression) acting together simultaneously against glyphosate.

Identifying Chloris Species from Cuban Citrus Orchards and Determining Their Glyphosate-Resistance Status

The Chloris genus is a C₄ photosynthetic species mainly distributed in tropical and subtropical regions. Populations of three Chloris species occurring in citrus orchards from central Cuba, under long history glyphosate-based weed management, were studied for glyphosate-resistant status by characterizing their herbicide resistance/tolerance mechanisms. Morphological and molecular analyses allowed these species to be identified as C. ciliata Sw., Chloris elata Desv., and Chloris barbata Sw. Based on the glyphosate rate that causes 50% mortality of the treated plants, glyphosate resistance (R) was confirmed only in C. elata, The R population was 6.1-fold more resistant compared to the susceptible (S) population. In addition, R plants of C. elata accumulated 4.6-fold less shikimate after glyphosate application than S plants. Meanwhile, populations of C. barbata and C. ciliata with or without glyphosate application histories showed similar LD₅₀ values and shikimic acid accumulation rates, demonstrating that resistance to glyphosate have not evolved in these species. Plants of R and S populations of C. elata differed in ¹⁴C-glyphosate absorption and translocation. The R population exhibited 27.3-fold greater 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) activity than the S population due to a target site mutation corresponding to a Pro-106-Ser substitution found in the EPSPS gene. These reports show the innate tolerance to glyphosate of C. barbata and C. ciliata, and confirm the resistance of C. elata to this herbicide, showing that both non-target site and target-site mechanisms are involved in its resistance to glyphosate. This is the first case of herbicide resistance in Cuba.