The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome-level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single-Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance-associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype-a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.

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.

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.

An ABCC-type transporter endowing glyphosate resistance in plants

Glyphosate is the most widely used herbicide in world agriculture and for general vegetation control in a wide range of situations. Global and often intensive glyphosate selection of very large weedy plant populations has resulted in widespread glyphosate resistance evolution in populations of many weed species. Here, working with a glyphosate-resistant (GR) Echinochloa colona population that evolved in a Western Australia agricultural field, we identified an ATP-binding cassette (ABC) transporter (EcABCC8) that is consistently up-regulated in GR plants. When expressed in transgenic rice, this EcABCC8 transporter endowed glyphosate resistance. Equally, rice, maize, and soybean overexpressing the EcABCC8 ortholog genes were made resistant to glyphosate. Conversely, CRISPR/Cas9-mediated knockout of the EcABCC8 ortholog gene OsABCC8 increased rice susceptibility to glyphosate. Subcellular localization analysis and quantification of glyphosate cellular levels in treated ABCC8 transgenic rice plants and isolated leaf protoplasts as well as structural modeling support that EcABCC8 is likely a plasma membrane-localized transporter extruding cytoplasmic glyphosate to the apoplast, lowering the cellular glyphosate level. This is a report of a membrane transporter effluxing glyphosate in a GR plant species, and its function is likely conserved in crop plant species.

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.

First case of glyphosate resistance in weedy sunflower (Helianthus annuus)

BACKGROUND

Weedy sunflower (Helianthus annuus L.) is a troublesome weed in row-crop production fields in South Texas. Populations with suspected resistance to glyphosate were evaluated with 1X and 4X rates (X = 868 g ae ha-1 ) of the herbicide, followed by a dose-response assay of the most resistant population. Molecular studies were conducted to determine if target-site mechanisms were responsible for resistance in these populations. Additionally, field experiments were conducted at two locations (Somerville and Granger, TX) to evaluate the effectiveness of different tank-mix combinations in controlling naturally infesting glyphosate-resistant (GR) weedy sunflower populations in GR corn.

RESULTS

In a study conducted in the growth chamber, seven of the 11 tested populations survived up to the 4X rate of glyphosate. The most-resistant population (TX15-11) was 29-fold more resistant to glyphosate, compared to the susceptible standard. In resistant populations, 5-21 more copies of the EPSPS gene were observed compared to the susceptible standard. In the field studies, tank-mix applications of glyphosate + halosulfuron-methyl, glyphosate + prosulfuron, glyphosate + a premix of halosulfuron-methyl and dicamba or glyphosate + a premix of diflufenzopyr and dicamba effectively controlled GR weedy sunflower populations.

CONCLUSION

Glyphosate-resistance was observed in 81% of the putative resistant weedy sunflower populations tested in this study. Resistance in these populations was conferred primarily by amplification of the EPSPS gene. Effective control of GR weedy sunflower can be achieved by tank-mixes tested in the current study, which provides acceptable levels of crop safety. © 2020 Society of Chemical Industry.

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.

Non-Target-Site Resistance to Herbicides: Recent Developments

Non-target-site resistance (NTSR) to herbicides in weeds can be conferred as a result of the alteration of one or more physiological processes, including herbicide absorption, translocation, sequestration, and metabolism. The mechanisms of NTSR are generally more complex to decipher than target-site resistance (TSR) and can impart cross-resistance to herbicides with different modes of action. Metabolism-based NTSR has been reported in many agriculturally important weeds, although reduced translocation and sequestration of herbicides has also been found in some weeds. This review focuses on summarizing the recent advances in our understanding of the physiological, biochemical, and molecular basis of NTSR mechanisms found in weed species. Further, the importance of examining the co-existence of TSR and NTSR for the same herbicide in the same weed species and influence of environmental conditions in the altering and selection of NTSR is also discussed. Knowledge of the prevalence of NTSR mechanisms and co-existing TSR and NTSR in weeds is crucial for designing sustainable weed management strategies to discourage the further evolution and selection of herbicide resistance in weeds.

Glyphosate resistance in Ambrosia trifida: Part 1. Novel rapid cell death response to glyphosate

BACKGROUND

Glyphosate-resistant (GR) Ambrosia trifida is now present in the midwestern United States and in southwestern Ontario, Canada. Two distinct GR phenotypes are known, including a rapid response (GR RR) phenotype, which exhibits cell death within hours after treatment, and a non-rapid response (GR NRR) phenotype. The mechanisms of resistance in both GR RR and GR NRR remain unknown. Here, we present a description of the RR phenotype and an investigation of target-site mechanisms on multiple A. trifida accessions.

RESULTS

Glyphosate resistance was confirmed in several accessions, and whole-plant levels of resistance ranged from 2.3- to 7.5-fold compared with glyphosate-susceptible (GS) accessions. The two GR phenotypes displayed similar levels of resistance, despite having dramatically different phenotypic responses to glyphosate. Glyphosate resistance was not associated with mutations in EPSPS sequence, increased EPSPS copy number, EPSPS quantity, or EPSPS activity.

CONCLUSION

These encompassing results suggest that resistance to glyphosate in these GR RR A. trifida accessions is not conferred by a target-site resistance mechanism. © 2017 Society of Chemical Industry.

Modeling pollen-mediated gene flow from glyphosate-resistant to -susceptible giant ragweed (Ambrosia trifida L.) under field conditions

A field experiment was conducted to quantify pollen mediated gene flow (PMGF) from glyphosate-resistant (GR) to glyphosate-susceptible (GS) giant ragweed under simulated field conditions using glyphosate resistance as a selective marker. Field experiments were conducted in a concentric design with the GR giant ragweed pollen source planted in the center and GS giant ragweed pollen receptors surrounding the center in eight directional blocks at specified distances (between 0.1 and 35 m in cardinal and ordinal directions; and additional 50 m for ordinal directions). Seeds of GS giant ragweed were harvested from the pollen receptor blocks and a total of 100,938 giant ragweed plants were screened with glyphosate applied at 2,520 g ae ha-1 and 16,813 plants confirmed resistant. The frequency of PMGF was fit to a double exponential decay model selected by information-theoretic criteria. The highest frequency of gene flow (0.43 to 0.60) was observed at ≤0.5 m from the pollen source and reduced rapidly with increasing distances; however, gene flow (0.03 to 0.04) was detected up to 50 m. The correlation between PMGF and wind parameters was inconsistent in magnitude, direction, and years.