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

Divergence in Glyphosate Susceptibility between Steinchisma laxum Populations Involves a Pro106Ser Mutation

The characterization of the mechanisms conferring resistance to herbicides in weeds is essential for developing effective management programs. This study was focused on characterizing the resistance level and the main mechanisms that confer resistance to glyphosate in a resistant (R) Steinchisma laxum population collected in a Colombian rice field in 2020. The R population exhibited 11.2 times higher resistance compared to a susceptible (S) population. Non-target site resistance (NTSR) mechanisms that reduced absorption and impaired translocation and glyphosate metabolism were not involved in the resistance to glyphosate in the R population. Evaluating the target site resistance mechanisms by means of enzymatic activity assays and EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) gene sequencing, the mutation Pro106Ser was found in R plants of S. laxum. These findings are crucial for managing the spread of S. laxum resistance in Colombia. To effectively control S. laxum in the future, it is imperative that farmers use herbicides with different mechanisms of action in addition to glyphosate and adopt Integrate Management Programs to control weeds in rice fields of the central valleys of Colombia.

Multiple Resistance Mechanisms Involved in Glyphosate Resistance in Eleusine indica

Glyphosate is a non-selective herbicide and is widely used for weed control in non-cultivated land in China. One susceptible (S) and five putative glyphosate-resistant (R1, R2, R3, R4, and R5) Eleusine indica biotypes were selected to investigate their resistance levels and the potential resistance mechanisms. Based on the dose-response assays, the R3 and R5 biotypes showed a low-level (2.4 to 3.5-fold) glyphosate resistance, and the R1, R2, and R4 biotypes exhibited a moderate- to high-level (8.6 to 19.2-fold) resistance, compared with the S biotype. The analysis of the target-site resistance (TSR) mechanism revealed that the P106A mutation and the heterozygous double T102I + P106S mutation were found in the R3 and R4 biotypes, respectively. In addition, the similar EPSPS gene overexpression was observed in the R1, R2, and R5 biotypes, suggesting that additional non-target-site resistance (NTSR) mechanisms may contribute to glyphosate resistance in R1 and R2 biotypes. Subsequently, an RNA-Seq analysis was performed to identify candidate genes involved in NTSR. In total, ten differentially expressed contigs between untreated S and R1 or R2 plants, and between glyphosate-treated S and R1 or R2 plants, were identified and further verified with RT-qPCR. One ATP-binding cassette (ABC) transporter gene, one aldo-keto reductases (AKRs) gene and one cytochrome P450 monooxygenase (CytP450) gene were up-regulated in R1 or R2 plants. These results indicated that EPSPS overexpression, single or double mutation was a common TSR mechanisms in E. indica. Additional NTSR mechanisms could play an essential role in glyphosate resistance. Three genes, ABCC4, AKR4C10, and CYP88, could serve as important candidate genes and deserve further functional studies.

The Molecular, Morphological and Genetic Characterization of Glyphosate Resistance in Conyza bonariensis from South Africa

Six Conyza bonariensis (L.) Cronquist populations were screened in a pot experiment at the University of Pretoria's Hatfield experimental farm to evaluate and confirm the degree of glyphosate response. Resistance factors ranged from 2.7- to 24.8-fold compared to the most susceptible biotype. Partial sequencing of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene found no mutation at the Thr102, Ala103 or Pro106 positions. EPSPS mRNA expression levels in glyphosate-resistant biotypes (Swellendam and Piketberg seed sampling sites) were comparable or lower than those in susceptible biotypes (George and Fauresmith sites). Additionally, the highest expression level was reported in the susceptible Fauresmith biotype. These results indicate that glyphosate resistance in the tested resistant biotypes is not caused by target-site mutations and EPSPS gene amplification. Leaf surface characteristics can influence the spread and subsequent absorption of glyphosate. The study established non-significant results in the amount of leaf wax and insufficient mean separations in cuticle thickness and trichome density data. Therefore, the observed differences in response of biotypes to glyphosate treatment could not be attributed conclusively to differences in the leaf morphological characteristics investigated. Results from the inheritance study were consistent with glyphosate resistance being inherited in an incompletely dominant manner when plants were treated with glyphosate herbicide at 900 g ae ha^-1.

Multiple herbicide resistance in Eleusine indica from sugarcane fields in China

Long-term reliance on herbicide weed control has led to resistance evolution in Eleusine indica in sugarcane fields of Guangxi Zhuang autonomous region. Ninety-six E. indica lines were collected from this region, and their response was tested to six herbicides: glyphosate; glufosinate; PSII-inhibitors diuron and atrazine; and PSI inhibitors paraquat and diquat. Target-site resistance mechanisms were examined in specific lines with multiple resistance to three herbicide modes of action. Of 96 E. indica lines, 51, 26, and 24 lines had resistance to diuron, atrazine, and diquat, respectively, while 14 and 9 had resistance to paraquat and glyphosate. Among 25 lines tested with multiple resistance, 7 lines exhibited resistance to three herbicide modes of action. In two multiple resistant lines (GXER2, GXER5), amplification/over-expression/mutations of the EPSPS gene contributed to the very high-level (up to 109-fold) glyphosate resistance. No target-site mutations/over-expression were identified in the psbA gene in these two lines, so non-target-site resistance mechanisms were likely responsible for the low-level (3-fold) resistance to the PSII herbicides diuron and atrazine. A high-level (23-fold) of paraquat resistance was observed in GXER5, and a low-level (5-fold) paraquat resistance was found in GXER2. Multiple herbicide resistance in E. indica has evolved in sugarcane fields of Guangxi Zhuang autonomous region with diverse resistance mechanisms. Therefore, diversified weed control tactics should be adopted to prevent this weed.

A Target-Site Mutation Confers Cross-Resistance to ALS-Inhibiting Herbicides in Erigeron sumatrensis from Brazil

Cases of weed resistant to herbicides have changed the dynamics of agricultural areas in Brazil, and in recent years, Erigeron species have caused major problems to farmers in the country, mainly in relation to the ineffectiveness of herbicide treatments used. The objective of this study was to confirm the cross-resistance to ALS inhibitors in populations of Erigeron sumatrensis as well as to investigate the existence of mutations in the site of action of ALS-inhibiting herbicides. To do this, 30 populations collected in the 2016/2017 crop season were grown in a greenhouse. Dose-response (chlorimuron-ethyl and cloransulam-methyl), inhibition of cytochrome P-450 with malathion, and ALS gene sequencing experiments were carried out in the F1 generations of two fleabane populations. The results proved the cross-resistance to chlorimuron-ethyl and cloransulam-methyl herbicides applied in the post-emergence of the resistant population of E. sumatrensis. The higher activity of P450 enzymes is unlikely responsible for the resistance of the population studied. The resistance mechanism found in R was the target site mutation Pro197Ser at the ALS gene. This is the first study in Brazil to identify a target-site change as a survival mechanism in E. sumatrensis for the resistance to ALS-inhibiting herbicides.

Biochemical Basis for the Time-of-Day Effect on Glufosinate Efficacy against Amaranthus palmeri

Glufosinate, a glutamine synthetase (GS) inhibitor, often provides variable weed control depending on environmental conditions such as light, temperature and humidity at the time of application. Midday applications normally provide improved efficacy compared to applications at dawn or dusk. We investigated the biochemical basis for the time-of-day effect on glufosinate efficacy in Amaranthus palmeri. GS1/GS2 gene expression and GS1/GS2 protein abundance were assessed in different parts (young leaves, old leaves, and roots) of plants incubated in the dark compared to those in the light. The turnover of GS total activity was also evaluated overtime following glufosinate treatment at midday compared to dusk application. The results suggest that GS in A. palmeri is less expressed and less abundant in the dark compared to in the light. Midday application of glufosinate under intense light conditions following application provide full control of A. palmeri plants. Consequently, these plants are unable to recover GS activity by de novo protein synthesis. Full activity of GS is required for complete inhibition by the irreversible inhibitor glufosinate. Therefore, glufosinate applications should always be performed in the middle of the day when sunlight is intense, to prevent weed escapes from the herbicide treatment.

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.

Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications

The treatment of environmental pollution by microorganisms and their enzymes is an innovative and socially acceptable alternative to traditional remediation approaches. Microbial biodegradation is often characterized with high efficiency as this process is catalyzed via degrading enzymes. Various naturally isolated microorganisms were demonstrated to have considerable ability to mitigate many environmental pollutants without external intervention. However, only a small fraction of these strains are studied in detail to reveal the mechanisms at the enzyme level, which strictly limited the enhancement of the degradation efficiency. Accordingly, this review will comprehensively summarize the function of various degrading enzymes with an emphasis on catalytic mechanisms. We also inspect the expanded applications of these pollutant-degrading enzymes in industrial processes. An in-depth understanding of the catalytic mechanism of enzymes will be beneficial for exploring and exploiting more degrading enzyme resources and thus ameliorate concerns associated with the ineffective biodegradation of recalcitrant and xenobiotic contaminants with the help of gene-editing technology and synthetic biology.

Survival on railway tracks of Geranium robertianum-a glyphosate-tolerant plant

Geranium robertianum is a herbaceous plant that prefers shady and fertile forest habitats. However, it also occurs on railway tracks, where there are difficult conditions for plant growth and regular herbicide spraying (in high concentrations, twice a year). One of the most commonly used herbicides in railway areas is glyphosate. The effect of the glyphosate on the G. robertianum plants found on railway tracks and in nearby forests in north-eastern Poland was checked. The aim of the study was to explain how G. robertianum can survive on railway tracks despite spraying with the glyphosate. Increased tolerance to the glyphosate of the G. robertianum plants from track populations was demonstrated compared to the plants from forest populations that had not previously been in contact with the herbicide. After 35 days after treatment with the herbicide, 75% of the plants from the observed forest populations withered, while only 38% did from the track populations. Ultrastructure of plant leaf cells from forest populations was strongly disturbed, which was not observed in plants from track populations. It was also shown that plants from track populations accumulated more glyphosate and AMPA in their tissues than plants from forest populations. The obtained results indicate that long-term use of herbicides may cause formation of biotypes of plants resistant to a given herbicide. This fact explains the possibility of G. robertianum occurring on railway tracks, despite spraying with the glyphosate. It is also a manifestation of microevolutionary processes.

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.

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.

Multiple mutations in the EPSPS and ALS genes of Amaranthus hybridus underlie resistance to glyphosate and ALS inhibitors

Amaranthus hybridus is one of the main weed species in Córdoba, Argentina. Until recently, this weed was effectively controlled with recurrent use of glyphosate. However, a population exhibiting multiple resistance (MR2) to glyphosate and imazamox appeared in a glyphosate resistant (GR) soybean field, with levels of resistance up to 93 and 38-fold higher to glyphosate and imazamox, respectively compared to the susceptible (S) population. In addition to imidazolinones, MR2 plants showed high resistance levels to sulfonylamino-carbonyl (thio) benzoates and moderate resistance to sulfonylureas and triazolopyrimidines. Multiple amino acid substitutions were found in both target genes, acetolactate synthase (ALS) and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), responsible for conferring high herbicides resistance levels in this A. hybridus population. In the case of EPSPS, the triple amino acid substitution TAP-IVS was found. In addition, MR2 plants also showed increased EPSPS gene expression compared to susceptible plants. A Ser653Asn substitution was found in the ALS sequence of MR2, explaining the pattern of cross-resistance to the ALS-inhibitor herbicide families found at the ALS enzyme activity level. No other mutations were found in other conserved domains of the ALS gene. This is the first report worldwide of the target site resistance mechanisms to glyphosate and ALS inhibitors in multiple herbicide resistance Amaranthus hybridus.

Resistance to Fomesafen, Imazamox and Glyphosate in Euphorbia heterophylla from Brazil

Euphorbia heterophylla is a species of weed that was previously controlled by fomesafen, imazamox and glyphosate, but continued use of these herbicides has selected resistant populations from the Rio Grande do Sul (Brazil). One resistant (R) strain and one susceptible (S) strain to fomesafen, imazamox and glyphosate were compared, the latter by recurrent selection. Dose-response tests showed multiple resistance to these herbicides. The required imazamox concentration to inhibit ALS by 50% was approximately 16 times greater in the R population than in the S population. Based on the EPSPS activity results, the R population was 10 fold less sensitive to glyphosate than the S counterpart. In addition, basal EPSPS activity from R plants was 3.3 fold higher than the level detected on S plants. The Proto IX assays showed high resistance to fomesafen in the R population that accumulated less Proto IX than the S population. Malathion assays showed the participation of CytP450 in fomesafen resistance, but a molecular mechanism could also be involved. To our knowledge, this is the first characterisation of multiple resistance to these three groups of herbicides in E. heterophylla in the world.

Evolution of EPSPS double mutation imparting glyphosate resistance in wild poinsettia (Euphorbia heterophylla L.)

The evolution of glyphosate resistance (GR) in weeds is an increasing problem. Glyphosate has been used intensively on wild poinsettia (Euphorbia heterophylla L.) populations for at least 20 years in GR crops within South America. We investigated the GR mechanisms in a wild poinsettia population from a soybean field in southern Brazil. The GR population required higher glyphosate doses to achieve 50% control (LD50) and 50% dry mass reduction (MR50) compared to a glyphosate susceptible (GS) population. The ratio between the LD50 and MR50 of GR and GS resulted in resistance factors (RF) of 6.9-fold and 6.1-fold, respectively. Shikimate accumulated 6.7 times more in GS than in GR when leaf-discs were incubated with increasing glyphosate concentrations. No differences were found between GR and GS regarding non-target-site mechanisms. Neither population metabolized glyphosate to significant levels following treatment with 850 g ha-1 glyphosate. Similar levels of 14C-glyphosate uptake and translocation were observed between the two populations. No differences in EPSPS expression were found between GS and GR. Two target site mutations were found in all EPSPS alleles of homozygous resistant plants: Thr102Ile + Pro106Thr (TIPT-mutation). Heterozygous individuals harbored both alleles, wild-type and TIPT. Half of GR individuals were heterozygous, suggesting that resistance is still evolving in the population. A genotyping assay was developed based on the Pro106Thr mutation, demonstrating high efficiency to identify homozygous, heterozygous or wild-type EPSPS sequences across different plants. This is the first report of glyphosate-resistant wild-poinsettia harboring an EPSPS double mutation (TIPT) in the same plant.

Mechanisms of evolved herbicide resistance

The widely successful use of synthetic herbicides over the past 70 years has imposed strong and widespread selection pressure, leading to the evolution of herbicide resistance in hundreds of weed species. Both target-site resistance (TSR) and nontarget-site resistance (NTSR) mechanisms have evolved to most herbicide classes. TSR often involves mutations in genes encoding the protein targets of herbicides, affecting the binding of the herbicide either at or near catalytic domains or in regions affecting access to them. Most of these mutations are nonsynonymous SNPs, but polymorphisms in more than one codon or entire codon deletions have also evolved. Some herbicides bind multiple proteins, making the evolution of TSR mechanisms more difficult. Increased amounts of protein target, by increased gene expression or by gene duplication, are an important, albeit less common, TSR mechanism. NTSR mechanisms include reduced absorption or translocation and increased sequestration or metabolic degradation. The mechanisms that can contribute to NTSR are complex and often involve genes that are members of large gene families. For example, enzymes involved in herbicide metabolism-based resistances include cytochromes P450, GSH S-transferases, glucosyl and other transferases, aryl acylamidase, and others. Both TSR and NTSR mechanisms can combine at the individual level to produce higher resistance levels. The vast array of herbicide-resistance mechanisms for generalist (NTSR) and specialist (TSR and some NTSR) adaptations that have evolved over a few decades illustrate the evolutionary resilience of weed populations to extreme selection pressures. These evolutionary processes drive herbicide and herbicide-resistant crop development and resistance management strategies.

A Trp574Leu Target-Site Mutation Confers Imazamox Resistance in Multiple Herbicide-Resistant Wild Poinsettia Populations from Brazil

Wild poinsettia (Euphorbia heterophylla L.) is an important weed species in southern Brazil, especially due to the evolution of multiple herbicide resistance (e.g., acetolactate synthase (ALS)- inhibitors, protoporphyrinogen oxidase inhibitors, and glyphosate). The mechanism of resistance to imazamox was investigated in two wild poinsettia populations (R1 and R2) from southern Brazil and compared to a known susceptible (S) population. Imazamox dose-response experiments revealed high levels of resistance: 45-fold and 224.5-fold based on dry biomass reduction, for R1 and R2, respectively. Extremely high concentrations of imazamox (20,000 µM) were not sufficient to provide 50% inhibition of ALS enzyme activity (I50) for R1 or R2. Hence, resistance levels were estimated to be greater than 123-fold for both populations based on in vitro ALS assays. The ALS gene from all R1 and R2 plants had a Trp574Leu mutation. A genotyping assay was developed to discriminate resistant and susceptible alleles based on the Trp574Leu mutation.

Target-Site Mutations Conferring Herbicide Resistance

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

Multiple Resistance to Synthetic Auxin Herbicides and Glyphosate in Parthenium hysterophorus Occurring in Citrus Orchards

Dominican farmers have started to apply synthetic auxin herbicides (SAHs) as the main alternative to mitigate the impacts of the occurrence of glyphosate-resistant (GR) Parthenium hysterophorus populations in citrus orchards. A GR P. hysterophorus population survived field labeled rates of glyphosate, 2,4-dichlorophenoxyacetic acid (2,4-D), dicamba, and picloram, which showed poor control (<50%). In in vivo assays, resistance levels were high for glyphosate and moderate for picloram, dicamba, and 2,4-D. Sequencing the 5-enolpyruvylshikimate-3-phosphate synthase gene revealed the double Thr-102-Ile and Pro-106-Ser amino acid substitution, conferring resistance to glyphosate. Additionally, reduced absorption and impaired translocation contributed to this resistance. Regarding SAH, impaired 2,4-D transport and enhanced metabolism were confirmed in resistant plants. The application of malathion improved the efficacy of SAHs (control >50%), showing that metabolism of these herbicides was mediated by cytochrome P450 enzymes. This study reports, for the first time, multiple resistance to SAHs and glyphosate in P. hysterophorus.