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BACKGROUND: Giant ragweed (Ambrosia trifida L.) is one of the most troublesome weed species in corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] cropping systems. Following numerous reports in 2018 of suspected herbicide resistance in several Ambrosia trifida populations from Wisconsin, our objective was to characterize the response of these accessions to acetolactate synthase (ALS), enolpyruvyl shikimate phosphate synthase (EPSPS), and protoporphyrinogen oxidase (PPO) inhibitors applied POST. RESULTS: Four accessions (AT1, AT4, AT6, and AT10) exhibited ≥ 50% plant survival after exposure to the cloransulam 3× rate. Two accessions (AT8 and AT10) and one accession (AT2) exhibited ≥ 50% plant survival after exposure to glyphosate and fomesafen 1× rates, respectively. The AT10 accession exhibited multiple resistance to cloransulam and glyphosate. The AT12 accession was 28.8‐fold resistant to fomesafen and 3.7‐fold resistant to lactofen. A codon change in PPX2 conferring a R98L substitution was identified as the most likely mechanism conferring PPO‐inhibitor resistance. CONCLUSION: To our knowledge, this is the first confirmed case of PPO‐inhibitor resistance in Ambrosia trifida globally and we identified the genetic mutation likely conferring resistance. Proactive and diversified integrated weed management strategies are of paramount importance for sustainable long‐term Ambrosia trifida management. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The emergence of herbicide‐resistant weeds is a significant threat to modern agriculture. Cross resistance, a phenomenon where resistance to one herbicide confers resistance to another, is a particular concern owing to its unpredictability. Nontarget‐site (NTS) cross resistance is especially challenging to predict, as it arises from genes that encode enzymes that do not directly involve the herbicide target site and can affect multiple herbicides. Recent advancements in genomic and structural biology techniques could provide new venues for predicting NTS resistance in weed species. In this review, we present an overview of the latest approaches that could be used. We discuss the use of genomic and epigenomics techniques such as ATAC‐seq and DAP‐seq to identify transcription factors and cis‐regulatory elements associated with resistance traits. Enzyme/protein structure prediction and docking analysis are discussed as an initial step for predicting herbicide binding affinities with key enzymes to identify candidates for subsequent in vitro validation. We also provide example analyses that can be deployed toward elucidating cross resistance and its regulatory patterns. Ultimately, our review provides important insights into the latest scientific advancements and potential directions for predicting and managing herbicide cross resistance in weeds. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

BACKGROUND: Target site resistance to herbicides that inhibit protoporphyrinogen IX oxidase (PPO; EC 1.3.3.4) has been described mainly in broadleaf weeds based on mutations in the gene designated protoporphyrinogen oxidase 2 (PPO2) and in one monocot weed species in protoporphyrinogen oxidase 1 (PPO1). To control PPO target site resistant weeds in future it is important to design new PPO-inhibiting herbicides that can control problematic weeds expressing mutant PPO enzymes. In this study, we assessed the efficacy of a new triazinone-type inhibitor, trifludimoxazin, to inhibit PPO2 enzymes carrying target site mutations in comparison with three widely used PPO-inhibiting herbicides. RESULTS: Mutated Amaranthus spp. PPO2 enzymes were expressed in Escherichia coli, purified and measured biochemically for activity and inhibition kinetics, and used for complementation experiments in an E. coli hemG mutant that lacks the corresponding microbial PPO gene function. In addition, we used ectopic expression in Arabidopsis and structural PPO protein modeling to support the enzyme inhibition study. The generated data strongly suggest that trifludimoxazin is a strong inhibitor both at the enzyme level and in transgenics Arabidopsis ectopically expressing PPO2 target site mutations. CONCLUSION: Trifludimoxazin is a potent PPO-inhibiting herbicide that inhibits various PPO2 enzymes carrying target site mutations and could be used as a chemical-based control strategy to mitigate the widespread occurrence of PPO target site resistance as well as weeds that have evolved resistance to other herbicide mode of actions. [ABSTRACT FROM AUTHOR]

BACKGROUND Amaranthus tuberculatus is a problematic weed species in Midwest USA agricultural systems. Inhibitors of 4‐hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD‐inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS: Dose–response studies of an F1 generation identified HPPD‐inhibitor resistance as a dominant trait with a resistance factor of 15.0–21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo‐F2 generation determined the trait is moderately heritable (H2 = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS: Resistance to HPPD inhibitors is a complex, largely dominant trait within the NEB population. Two large‐effect QTL were identified controlling HPPD‐inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species. [ABSTRACT FROM AUTHOR]

Amaranthus tuberculatus is the major weed species in many midwestern US row‐crop production fields, and it is among the most problematic weeds in the world in terms of its ability to evolve herbicide resistance. It has now evolved resistance to herbicides spanning seven unique sites of action, with populations and even individual plants often possessing resistance to several herbicides/herbicide groups. Historically, herbicide target‐site changes accounted for most of the known resistance mechanisms in this weed; however, over the last few years, non‐target‐site mechanisms, particularly enhanced herbicide detoxification, have become extremely common in A. tuberculatus. Unravelling the genetics and molecular details of non‐target‐site resistance mechanisms, understanding the extent to which they confer cross resistance to other herbicides, and understanding how they evolve remain as critical research endeavors. Transcriptomic and genomics approaches are already facilitating such studies, the results of which hopefully will inform better resistance‐mitigation strategies. The largely unprecedented level of herbicide resistance in A. tuberculatus is not only a fascinating example of evolution in action, but it is a serious and growing threat to the sustainability of midwestern US cropping systems. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Abstract: Protoporphyrinogen IX oxidase (PPO)‐inhibiting herbicides are effective tools to control a broad spectrum of weeds, including those that have evolved resistance to glyphosate. Their utility is being threatened by the appearance of biotypes that are resistant to PPO inhibitors. While the chloroplastic PPO1 isoform is thought to be the primary target of PPO herbicides, evolved resistance mechanisms elucidated to date are associated with changes to the mitochondrial PPO2 isoform, suggesting that the importance of PPO2 has been underestimated. Our investigation of the evolutionary and structural biology of plant PPOs provides some insight into the potential reasons why PPO2 is the preferred target for evolution of resistance. The most common target‐site mutation imparting resistance involved the deletion of a key glycine codon. The genetic environment that facilitates this deletion is apparently only present in the gene encoding PPO2 in a few species. Additionally, both species with this mutation (Amaranthus tuberculatus and Amaranthus palmeri) have dual targeting of PPO2 to both the chloroplast and the mitochondria, which might be a prerequisite to impart herbicide resistance. The most recent target‐site mutations have substituted a key arginine residue involved in stabilizing the substrate in the catalytic domain of PPO2. This arginine is highly conserved across all plant PPOs, suggesting that its substitution could be equally likely on PPO1 and PPO2, yet it has only occurred on PPO2, underscoring the importance of this isoform for the evolution of herbicide resistance. © 2017 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

BACKGROUND The fitness cost of herbicide resistance (HR) in the absence of herbicide selection plays a key role in HR evolution. Quantifying the fitness cost of resistance, however, is challenging, and there exists a knowledge gap in this area. A synthetic (artificially generated) Amaranthus tuberculatus population segregating for five types of HR was subjected to competitive growth conditions in the absence of herbicide selection for six generations. Fitness costs were quantified by using a combination of phenotyping and genotyping to monitor HR frequency changes over generations. RESULTS In the absence of herbicide selection, a significant fitness cost was observed for resistance to acetolactate synthase-inhibiting herbicides, but not for resistances to atrazine (non-target-site resistance mechanism), protoporphyrinogen oxidase inhibitors, 4-hydroxyphenylpryuvate dioxygenase inhibitors or glyphosate. Glyphosate resistance was conferred by multiple mechanisms in the synthetic population, and further analysis revealed that one mechanism, amplification of the 5-enolypyruvylshikimate-3-phosphate synthase gene, did decrease in frequency. CONCLUSION Our results indicate that herbicide-resistance mitigation strategies (e.g. herbicide rotation) that rely on the existence of fitness costs in the absence of herbicide selection likely will be largely ineffective in many cases. © 2017 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

BACKGROUND: Understanding andmanaging the evolutionary responses of pests and pathogens to control efforts is essential to human health and survival. Herbicide-resistant (HR) weeds undermine agricultural sustainability, productivity and profitability, yet the epidemiology of resistance evolution - particularly at landscape scales - is poorly understood. We studied glyphosate resistance in amajor agriculturalweed, Amaranthus tuberculatus (commonwaterhemp), using landscape, weed and management data from 105 central Illinois grain farms, including over 500 site-years of herbicide application records. RESULTS: Glyphosate-resistant (GR) A. tuberculatus occurrencewas greatest in fieldswith frequent glyphosate applications, high annual rates of herbicidemechanism of action (MOA) turnover and few MOAs field-1 year-1. Combining herbicide MOAs at the time of application by herbicide mixing reduced the likelihood of GR A. tuberculatus. CONCLUSIONS: These findings illustrate the importance of examining large-scale evolutionary processes at relevant spatial scales. Although measures such as herbicide mixing may delay GR or other HR weed traits, they are unlikely to prevent them. Long-term weed management will require truly diversified management practices that minimize selection for herbicide resistance traits. [ABSTRACT FROM AUTHOR]

The article presents a study on the transcriptome sequencing of horseweed or Conyza Canadensis using GS-FLX 454. The study uses RNA extraction which was done through TriReagent according to the manufacturer's protocol, and sequencing data trimming and assembling which use CAP3 and EGassembler, and was annotated by the similarity search of three protein databases. The result shows that sequencing through GS-FLX 454 of weed species is a powerful and cost-effective platform.

While surveying Illinois Amaranthus tuberculatus (Moq) Sauer (tall waterhemp) half-sib populations for herbicide response variability, several were observed to segregate for resistance to atrazine. Studies were conducted on greenhouse-grown A tuberculatus plants to compare atrazine responses among populations that were segregating for resistance (SegR), uniformly sensitive (UniS) or uniformly resistant (UniR). In chlorophyll fluorescence assays, leaves of plants from the SegR and UniS populations displayed changes in fluorescence after treatment with atrazine, indicating that atrazine was inhibiting electron transport of photosystem II in chloroplasts. Sequencing of a fragment of psbA, which encodes the D1 protein, revealed that the SegR population did not contain the amino acid substitution that is typically found in triazine-resistant plants. Whole-plant herbicide dose-response experiments revealed that, relative to the UniS populations atrazine resistances in the UniR and SegR populations were >770-fold and 16-fold, respectively. The SegR population was also resistant to cyanazine (59-fold), but not to metribuzin, linuron or pyridate. Triazine resistance in the SegR population was shown to be a nuclear inherited traits unlike maternal inheritance of site-of-action mediated triazine resistance found in the UniR population. Taken collectively, these findings confirm the existence of two distinct triazine resistance mechanisms in A tuberculatus. [ABSTRACT FROM AUTHOR]

Amaranthus tuberculatus is the major weed species in many midwestern US row-crop production fields, and it is among the most problematic weeds in the world in terms of its ability to evolve herbicide resistance. It has now evolved resistance to herbicides spanning seven unique sites of action, with populations and even individual plants often possessing resistance to several herbicides/herbicide groups. Historically, herbicide target-site changes accounted for most of the known resistance mechanisms in this weed; however, over the last few years, non-target-site mechanisms, particularly enhanced herbicide detoxification, have become extremely common in A. tuberculatus. Unravelling the genetics and molecular details of non-target-site resistance mechanisms, understanding the extent to which they confer cross resistance to other herbicides, and understanding how they evolve remain as critical research endeavors. Transcriptomic and genomics approaches are already facilitating such studies, the results of which hopefully will inform better resistance-mitigation strategies. The largely unprecedented level of herbicide resistance in A. tuberculatus is not only a fascinating example of evolution in action, but it is a serious and growing threat to the sustainability of midwestern US cropping systems. © 2020 Society of Chemical Industry., (© 2020 Society of Chemical Industry.)