Biology subjects

Lerchl, J.

Publications and source records attributed to Lerchl, J..

9 recordsLinked to original sources

bioRxiv2026

Fendioxypyracil Exhibits Potent Inhibition of PPO-Resistant Mutant Enzymes and Robust Activity Against PPO-Resistant Amaranthus

Background: Resistance to protoporphyrinogen oxidase (PPO) inhibiting herbicides is mainly driven by diverse target-site mutations, reducing the effectiveness of this site of action in row crop systems. Fendioxypyracil is a newly developed PPO inhibitor with high intrinsic grass and broadleaf activity, but its performance against resistant populations and target-site enzyme variants remains insufficiently characterized. Results: Enzyme assays using PPO2 from Amaranthus palmeri and Setaria viridis demonstrated that fendioxypyracil maintained low IC50 values across a broad range of resistance associated mutations, including dG210 deletion and G210, R128, and G399 substitutions, whereas oxadiazon, tiafenacil, and saflufenacil showed substantial loss of potency. Greenhouse dose response experiments confirmed strong fendioxypyracil efficacy, with susceptible and G399A populations controlled at <3 g ai/ha, while dG210 and R128G populations showed only moderate shifts in sensitivity but remained effectively controlled at the recommended rate. Transgenic Arabidopsis thaliana expressing resistant PPX2 alleles exhibited faster and more severe injury with fendioxypyracil compared to saflufenacil. Field trials conducted in a PPO resistant Amaranthus palmeri population demonstrated that fendioxypyracil provided consistent weed control and density reduction, matching the performance of trifludimoxazin and saflufenacil while exceeding that of fomesafen. Conclusion: Fendioxypyracil provides robust and broad-spectrum activity against PPO resistant Amaranthus populations and target mutant enzymes, maintaining efficacy across diverse mutation backgrounds. These results demonstrate its potential as an effective tool for managing PPO inhibitor resistance and sustaining weed control in row-crop production systems.

molecular biology↗

bioRxiv2026

Characterization of a novel R98Q mutation that confers resistance to sulfentrazone in common ragweed (Ambrosia artemisiifolia) populations from MichiganShort title: PPO resistance in common ragweed

BACKGROUNDIn 2023, soybean growers in Eaton County, Michigan, reported repeated failures to control common ragweed (Ambrosia artemisiifolia L.) with (PPO)-inhibiting herbicides, sulfentrazone and fomesafen, in non-genetically modified soybeans. This study aimed to investigate resistance levels and mechanisms of resistance in two suspected resistant populations (R1 and R2). RESULTSDose-response assays revealed resistance to sulfentrazone in both populations, with LD50 values 24 and 36-fold higher than the susceptible population and reduced sensitivity to fomesafen. Nanopore sequencing identified two PPO2 target-site substitutions at codon 98: Arg- 98-Leu (R98L) and a novel Arg-98-Gln (R98Q) mutation. Both substitutions were associated with reduced herbicide binding affinity in computational modelling simulations. R98Q substitution conferred strong and selective resistance in the PPO2 enzyme inhibition assays, supporting its role as a key resistance mechanism. CONCLUSIONThis study reports the first field occurrence of the R98Q substitution in PPO2 of A. artemisiifolia populations and demonstrates its association with to PPO inhibitor resistance. These findings highlight the rapid evolution of target-site resistance and the need for continued monitoring and rapid diagnostic tools to detect emerging mutations. Further research is needed to clarify the contribution of additional resistance mechanisms.

plant biology↗

bioRxiv2026

Biochemical Characterization of Fatty Acid Thioesterase Target Site Mutants and their Implication on Herbicide Resistance

Herbicide resistance threatens effective weed control in modern agriculture, particularly in grass weeds such as Alopecurus myosuroides and Lolium multiflorum. Cinmethylin is a pre-emergence herbicide with a novel mode of action that inhibits plastidial fatty acid thioesterases (FATs), enzymes essential for fatty acid biosynthesis. Although no cases of field resistance to cinmethylin have been reported, its resistance risk has not been fully assessed. In this study, we biochemically characterized defined amino acid substitutions in FAT A and FAT B to evaluate their effects on cinmethylin inhibition profile. Some substitutions in FAT A reduced inhibition in vitro, with mutations at residue R171 causing the largest shifts in sensitivity. However, these highly resistant variants required multiple specific nucleotide polymorphisms and are therefore predicted to be unlikely to arise in weed populations. In FAT B, sensitivity shifts were generally moderate. Importantly, most substitutions that reduced cinmethylin sensitivity also impaired enzymatic activity, suggesting limited viability in planta. Overall, these results indicate that while theoretical target-site resistance mechanisms exist, the practical risk of rapid resistance evolution to cinmethylin is low, supporting its value for integrated grass weed management

biochemistry↗

bioRxiv2026

Novel Protoporphyrinogen oxidase 1 mutations endow resistance to PPO-inhibiting herbicides in Bassia scoparia

PPO-inhibiting herbicides are widely used to manage weeds in different cropping systems, yet resistance evolution threatens their long-term efficacy. Here, we investigated the molecular basis of resistance to PPO-inhibiting herbicides in Bassia scoparia biotypes collected from four locations in North Dakota, USA. Greenhouse dose-response assays revealed high levels of resistance to saflufenacil and carfentrazone-ethyl, while fomesafen retained full efficacy across all biotypes. Resistant plants did not show increased copy number or elevated expression of PPO1 or PPO2. Sequencing of survivor plants revealed conserved PPO2 sequences, but consistent target-site substitutions at position F454 in PPO1, including F454I, F454L, and F454V. In vitro enzyme assays demonstrated that these substitutions impair PPO1 sensitivity to saflufenacil and carfentrazone-ethyl, but not to fomesafen. Ectopic expression of B. scoparia PPO1 F454 mutant variants in Arabidopsis thaliana conferred tolerance to saflufenacil and carfentrazone-ethyl, but not to fomesafen, supporting greenhouse and in vitro results. Molecular modeling indicated that the conformational flexibility and interaction profile of fomesafen enables it to maintain binding to mutated PPO1 variants, in contrast to the more rigid structures of saflufenacil and carfentrazone-ethyl. A yeast-based complementation system further confirmed that F454 substitutions decrease herbicide sensitivity. In addition, developmental profiling showed distinct expression patterns of PPO1 and PPO2 during early growth stages in B. scoparia and Amaranthus spp., highlighting isoform-specific roles. Together, these findings represent the first reported PPO1 target-site mutations in a broadleaf weed species as a key mechanism of resistance and highlight that fomesafen is effective to control resistant B. scoparia populations.

biochemistry↗

bioRxiv2025

Analysis of glutamine synthetase target-site mutations and their role in endowing glufosinate-ammonium resistance

Glufosinate-ammonium (GFA) is a key non-selective herbicide for controlling Amaranthus palmeri and other weeds by targeting glutamine synthetase (GS). GS copy number, expression, sequence polymorphisms, and enzymatic properties in a GFA-resistant population (CCR) were studied. Digital PCR revealed no major GS amplification or target upregulation: most CCR plants had copy numbers and expression comparable to the susceptible reference, with only minor increases in GS2.1 and GS2.2 in a few individuals. Sequencing identified a non-synonymous substitution, G255D, in GS2.2 within a conserved region adjacent to the GFA-binding site. G255D retained [~]58% of wild-type activity in vitro assays, but was completely insensitive to GFA, with no measurable inhibition at tested concentrations. However, ectopic expression of G255D in Arabidopsis thaliana did not confer GFA tolerance, indicating the mutation alone is insufficient for resistance. In vitro analysis of the Eleusine indica GS1.1 S59G substitution revealed increased catalytic activity without affecting GFA sensitivity. A mutational panel of GS1.1 variants showed that substitutions at E131, E192, G245, H249, R291, R311, and R332 abolished enzyme activity or inhibitor sensitivity, with most variants retaining <2% of wild-type function. Among a broader set of predicted GS1.1 variants, high resistance indices were consistently linked to strong reductions in catalytic efficiency, underscoring the fitness costs of target-site alterations. Collectively, GS2.2 G255D appears to be a rare substitution combining substantial residual activity with complete GFA insensitivity and suggest that resistance via target-site modifications studied is constrained by trade-offs between catalytic function and herbicide binding.

biochemistry↗

bioRxiv2024

Extrachromosomal DNA-mediated glutamine synthetase 2 (GS2) amplification enables glufosinate resistance in Amaranthus palmeri

BackgroundPalmer amaranth achieves resistance to glufosinate by overproducing the chloroplastic glutamine synthetase (GS2) protein, a result of the amplification and overexpression of its nuclear coding gene. This study examined how amplified GS2 copies are inherited, identified their physical location in the cell, and investigated the mechanism of GS2 amplification. ResultsSegregation analysis revealed that inheritance of amplified GS2 copies deviates from classical Mendelian patterns, with poor correlation between plant level resistance and GS2 amplification. Fluorescence in situ hybridization revealed chromosomal insertions of GS2 and potential extrachromosomal circular DNA (eccDNA), and variability in GS2 amplification both among individual plants and within cells (not all cells in plants with high GS2 copy number showed GS2 amplification). The unpredictable inheritance patterns and distribution of GS2 copies across multiple chromosomes suggest a role for eccDNA in GS2 amplification. This was confirmed through eccDNA sequencing, which also identified multiple isoforms of GS2. ConclusionThis is the second documented case of herbicide resistance conferred by eccDNA-mediated target-site gene amplification in Palmer amaranth.

genomics↗

bioRxiv2024

A Novel Genomic Rearrangement in the Amaranthus palmeri Extrachromosomal Circular DNA Provides Dual Herbicide Resistance to Glyphosate and Glufosinate

Amplification of chloroplastic glutamine synthetase (GS2) has been characterized as one of the resistance mechanisms in glufosinate-resistant Amaranthus palmeri accession (MSR2). Previously, the overamplification of the glyphosate-resistance gene, 5-enolpyruvylshikimate-3-phosphate (EPSPS), in A. palmeri was determined to be driven by an extrachromosomal circular DNA (eccDNA). Here, a novel eccDNA is described that carries both glyphosate and glufosinate-ammonium target site due to co-duplication of their chromosomic native region, conferring resistance. Besides EPSPS, the novel replicon has a region replaced by a fragment carrying the GS2 isoforms (GS2.1 and GS2.2) and other genes. The co-existence of eccDNA carrying only EPSPS was confirmed in MSR2 samples harboring dual targeting eccDNA. The genomic structure of GS2 and EPSPS amplification was also assessed in a different glufosinate-resistant A. palmeri accession (MSR1) along with MSR2. The accessions showed distinct GS2.1 and GS2.2 amplification patterns suggesting the existence of diverse replicons that were not assembled here. The EPSPS was amplified in both accessions, and a correlation was observed with the GS2 isoforms in MSR2, further supporting the co-existence of these genes in the same replicon. These findings shed light on the complexity of eccDNA formation in plant systems, with the collection and accumulation of extra pieces of DNA.

genomics↗

bioRxiv2023

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

genomics↗

bioRxiv2021

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

evolutionary biology↗