Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover?

Appearance of transient heteromorphic large chromosome in glyphosate-resistant Amaranthus tuberculatus

Glyphosate resistance in crop weeds is commonly attributed to rapid evolution through the amplification of the target gene, EPSPS (5-enolpyruvylshikimate-3-phosphate synthase). This amplification typically occurs through mechanisms such as unequal recombination, segmental duplications within the target chromosome, or the formation of ring chromosomes and extrachromosomal circular (ecc) DNA elements containing EPSPS. However, structural abnormalities in chromosomes not directly associated with EPSPS amplification have not been documented in the glyphosate-resistant weed population. Here, we describe the presence of a large chromosome found exclusively in the glyphosate-resistant Amaranthus tuberculatus (waterhemp) population but absent in susceptible counterparts. This large chromosome (~ 6 μm) is approximately twice the size of normal chromosomes (~ 2-3 μm) and is present in both male and female euploid plants (2n = 32) in a heteromorphic state. It aroses through pericentromeric heterochromatin expansion and duplications of the 5S rDNA locus but notably lacks the EPSPS gene. The large chromosome pairs with its normal homolog but was not transmitted to progeny in controlled greenhouse matings, suggesting a fitness cost in the absence of glyphosate selection pressure. This large chromosome offers a potential resource for the investigation of chromosome evolution of adaptive traits for glyphosate resistance in A. tuberculatus.

Characterization of the Giant Foxtail's (Setaria faberi) ALS Gene and Its Enhanced Metabolism-Based Cross-Resistance to Nicosulfuron and Rimsulfuron

BACKGROUND

Weed herbicide resistance is a serious problem in crop protection globally. Giant foxtail (Setaria faberi R.A.N. Herrm.) populations cannot be controlled by acetolactate synthase (ALS)-inhibiting herbicides in a few corn (Zea mays L.) monoculture fields.

METHODS

Five putative resistant giant foxtail populations, originating from corn monoculture fields in northeastern Greece, were evaluated for possible evolution of ALS-inhibitor resistance (nicosulfuron, rimsulfuron). The resistance ratio, the underlying resistance mechanism, and its impact on competitive ability against corn were studied.

RESULTS

The whole-plant rate-response assays showed that these populations were resistant (R) to the sulfonylureas nicosulfuron and rimsulfuron, but susceptible (S) to imidazolinone imazamox, triketone 4-hydroxyphenylpyruvate dioxygenase inhibitor tembotrione, and acetyl-CoA carboxylase inhibitor cycloxydim. The sequencing of the ALS gene did not reveal the presence of resistance-associated point mutations, indicating that the resistance was probably not target-site mediated. This was confirmed by the application of piperonyl butoxide two hours before nicosulfuron application, which reversed the resistance in all R giant foxtail populations, supporting the evidence of enhanced metabolism-mediated resistance. The competition study between corn and R or S giant foxtail populations indicated no stable trend reduction in corn traits, suggesting that the resistance mechanism was not associated with the competitive ability of the R populations. The novel ALS genotype in S. faberi, characterized for the first time and submitted to the GenBank database with accession number PV016837, indicated a closer genetic relationship with the S. viridis ALS gene than with S. italica.

CONCLUSIONS

Five giant foxtail populations have evolved metabolism-based resistance to the ALS-inhibiting herbicides nicosulfuron and rimsulfuron.

Overexpressing of GT8 confers resistance to fenoxaprop-P-ethyl in Alopecurus japonicus

BACKGROUND

Alopecurus japonicus is one of the most predominant weeds in wheat fields across China, where significant herbicide resistance has emerged over the past decade.

RESULTS

When compared to the susceptible (S) population, the resistant (R) population exhibited a 9.48-fold increase in resistance to fenoxaprop-P-ethyl. The R population displayed cross-resistance to haloxyfop-P-methyl, quizalofop-P-ethyl, clodinafop-propargyl, sethoxydim, clethodim and pinoxaden. No known resistance mutations or overexpression of ACCase were detected in the R population. The R population showed enhanced metabolism of fenoxaprop-P-ethyl, as evidenced by high-performance liquid chromatography analysis. The cytochrome P450 (CYP450) inhibitor malathion and the glutathione-S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) partially reversed resistance to fenoxaprop-P-ethyl in the R population. Six upregulated genes were identified via RNA-sequencing, including two CYP450 genes (CYP86B1 and CYP71C1), one GST gene (GSTT1) and three glycosyl transferase (GT) genes (UGT73C, GT8 and CGT). Specifically, the expression of GT8 in yeast decreased sensitivity to fenoxaprop-P-ethyl, suggesting its potential involvement in herbicide metabolism. Molecular docking analysis further suggests that GT8 may be involved in herbicide metabolism.

CONCLUSION

Our findings not only identified GT8 as partially responsible for the resistance of A. japonicus to fenoxaprop-P-ethyl, but also provide a valuable resource for crop genetic engineering. These insights also could inform the development of effective management strategies for A. japonicus. © 2025 Society of Chemical Industry.

Meeting Report on the Symposium "Evolutionary Applications" at the 3rd Joint Congress on Evolutionary Biology

The symposium "Evolutionary Applications" took place on June 28, 2024 in the virtual part of the 3rd Joint Congress on Evolutionary Biology. It was contributed to the conference by the European Society for Evolutionary Biology (ESEB). The symposium highlighted research on evolutionary biology applied to address questions and contemporary problems in medicine and public health, conservation biology, and food production and agriculture. Each of the six talks covered a different application and a different organism: domestication of cheese-making fungi, restoration of long-lived bird populations, evolution of herbicide resistance, coral reef conservation, gene drive systems targeting Malaria vectors, and antibiotic resistance evolution in bacteria. By including speakers who are active in a consortium or work in an NGO, the symposium also showed how to make the step from scientific findings to practical application. The symposium furthermore featured a range of scientific methods, ranging from genomic analyses and mathematical modeling to laboratory evolution and field experiments. Speakers from across 15 time zones highlighted the potential of virtual symposia to foster global collaboration in evolutionary biology.

Re-exploration of phenolic compounds from natural waste rice husks: Combined synthesis of novel herbicide and evaluation of herbicidal activity

In a global context, weed management has emerged as a significant challenge in agricultural production, causing substantial economic losses annually. Consequently, the development of innovative and efficient herbicides is crucial. Natural products serve as important sources for discovering novel herbicides. Through chemical synthesis and structural modification of natural compounds, novel herbicides can be developed. Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX, a critical step in the biosynthesis of porphyrins. PPO inhibitors target protoporphyrinogen oxidase, inhibiting its activity and thereby blocking porphyrin biosynthesis, ultimately leading to plant death. In this research, protoporphyrinogen oxidase was targeted, and monomeric compounds were extracted from natural rice husks, followed by selective manipulation to design and synthesize 33 new compounds. Weed control assays (37.5-300 g ai/ha) showed that most of the new compounds exhibited significant herbicidal activity against dicot weeds, but less effectiveness against monocot weeds. In particular, compound I-c4 demonstrated excellent post-emergence herbicidal activity on six weed species, comparable to the commercial herbicide oxyfluorfen. Activity experiments showed that compound I-c4 significantly reduced PPO levels in weeds. Molecular docking results indicated that compound I-c4 effectively occupies the substrate pocket of PPO enzymes, demonstrating strong inhibitory effects on receptor protein activity. Thus, compound I-c4 shows promise as a novel PPO herbicide for effective weed control.

The importance of developing an integrated data-driven modelling platform for herbicide resistance research: A review

Herbicide-resistant weeds pose a global challenge, constraining agricultural practices worldwide. Despite efforts to establish an integrated, data-driven framework, understanding the varied risks of herbicide resistance (HR) across different agroecological zones remains elusive. This review paper advocates for an integrated approach that incorporates socioeconomic, environmental, adoption behavior, and physiological factors to uncover insights into HR drivers and develop tailored management strategies. HR not only escalates production costs but also necessitates alternative weed management tactics, highlighting the urgency for proactive environmental management to mitigate soil health degradation and biodiversity loss. While current initiatives prioritize integrated weed management (IWM) like crop rotation and herbicide mixtures, challenges persist in integrating socioeconomic factors into predictive models and promoting the universal adoption of sustainable practices. Advancements in big data analytics, spatial modeling, and remote sensing offer promising avenues for predicting and managing HR across landscapes. This study proposes a research framework to predict the emergence and management of HR in agri-food systems. Additionally, the study utilizes a novel text-mining technique to conduct a comprehensive literature review, highlighting gaps in the development of data-driven modeling platforms for predicting HR emergence. The text mining findings explored that while common terms like weeds, resistance, herbicides, crops, management, and control are prevalent, research often lacks focus on predictive data-driven approaches for HR. Therefore, urgent development of an integrated national-scale approach to predict HR emergence is imperative. Global cooperation is essential for sharing best practices, data, and responses to emerging resistance threats.

Different nontarget-site mechanisms underlie resistance to dicamba and 2,4-D in an Amaranthus tuberculatus population

BACKGROUND

Amaranthus tuberculatus (Moq.) Sauer (waterhemp) has emerged as one of several weed species that is resistant to synthetic auxin herbicides (SAHs). Among the mechanisms of resistance to SAHs, nontarget-site resistance (NTSR) has been of particular concern owing to its complexity. Here, we integrated linkage mapping with transcriptome analysis to explore NTSR mechanisms to two SAHs, dicamba and 2,4-D, in a multiple-herbicide-resistant A. tuberculatus population (CHR).

RESULTS

Phenotypic evaluations of an F2 mapping population indicated a polygenic basis for both dicamba and 2,4-D resistance in CHR. A weak correlation was observed between phenotypic responses to dicamba and 2,4-D treatments. Linkage mapping analyses revealed eight quantitative trait loci (QTL) regions associated with dicamba and 2,4-D resistance mapped to seven A. tuberculatus chromosomes. Together, these QTL regions explained 24.2 and 23.1% of the variation in dicamba- and 2,4-D-resistant phenotypes, respectively. Only one co-localized QTL region was found between the two resistance traits.

CONCLUSION

The results of this study demonstrated that resistance to dicamba and 2,4-D in the CHR population is under the control of genes at multiple loci. The weak phenotypic and genetic associations of resistance traits indicate that more than one NTSR mechanism confers resistance to dicamba and 2,4-D in this A. tuberculatus population. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Off-target drift of the herbicide dicamba disrupts plant-pollinator interactions via novel pathways

While herbicide use in agriculture is expected to have many effects on surrounding weed communities, it is largely unknown how plant exposure to sublethal doses of herbicide may subsequently impact plant-pollinator interactions. We tested the hypothesis that sublethal herbicide exposure indirectly alters plant-pollinator interactions through changes in plant traits, and specifically through alterations in floral display. Using a common garden experiment, we exposed 11 weed species to the herbicide dicamba and examined the potential for changes in pollinator abundance and patterns of pollinator visitation as well as alterations to plant traits. We found variation among plant species in the extent of damage from dicamba drift, and variation in size, flowering time, and flower displays, with some plant species showing negative impacts and others showing little effect. Pollinator frequencies were reduced in dicamba-exposed plots, and pollinator visits were reduced for some weed species yet not for others. Structural equation modeling revealed that the relationship between flower display and pollinator visits was disrupted in the presence of dicamba. Our study provides the most comprehensive picture to date of the impacts of herbicide drift on plant-pollinator interactions, with findings that highlight an underappreciated role of services supplied by weedy communities.

Chromosome-level genome assembly of Cyperus iria, an aggressive weed of rice

Cyperus iria is an aggressive weed of rice throughout the world. Until now, the reference genome of C. iria has not been published. Here, we completed the chromosome-level genome assembly of C. iria based on Illumina, PacBio and Hi-C reads. The assembled genome size of C. iria was 479.08 Mb with a contig N50 of 7.02 Mb. 68 pseudochromosomes were produced using Hi-C scaffolding, accounting for 99.65% of the assembled genome. The number of predicted protein-coding genes is 47,395, of which 93.26% were annotated, and 37.69% repetitive sequences were identified. Our study provided a valuable genomic resource for the molecular biology research and the management of C. iria.

Herbicidal interference: glyphosate drives both the ecology and evolution of plant-herbivore interactions

The coevolution of plants and their insect herbivores reflects eco-evolutionary dynamics at work - ecological interactions influence adaptive traits, which feed back to shape the broader ecological community. However, novel anthropogenic stressors like herbicide, which are strong selective agents, can disrupt these dynamics. Little is known about how the evolution of herbicide resistance may impact plant-herbivore interactions. We performed a common garden field experiment using Ipomoea purpurea (common morning glory) and the herbicide glyphosate (Roundup) to investigate the ecological effects of herbicide exposure on insect herbivory patterns and assess the potential evolutionary consequences. We find that plants treated with glyphosate experienced higher levels of herbivory and altered chewing herbivory damage patterns. Additionally, we found that glyphosate resistance is positively associated with herbivory resistance, and uncovered positive selection for increased glyphosate resistance, suggesting that selection for increased glyphosate resistance has the potential to lead to increased herbivory resistance. Positive selection for glyphosate resistance, coupled with the detection of genetic variation for this trait, suggests there is potential for glyphosate resistance - and herbivory resistance via hitchhiking - to further evolve. Our results show that herbicides cannot just influence, but potentially drive the eco-evolutionary dynamics of plant-herbivore interactions.

Use of by-products from the industrial distillation of lavandin (Lavandula x intermedia) essential oil as effective bioherbicides

Weeds are one of the main problems causing losses in agricultural crops, which are nowadays mainly combated by the massive use of chemical herbicides. The development of new effective, sustainable, environmentally and health-friendly bioherbicides is a fundamental need worldwide. In this work, hydrolates and lavandin distilled straws produced during the distillation of the essential oil of lavandin (Lavandula x intermedia) were tested as potential bioherbicides. The weeds used were brome, annual ryegrass (monocotyledons), goosefoot and mat amaranth (dicotyledons) and the crops wheat, barley (monocotyledons), lentil and vetch (dicotyledons). The herbicidal capacity of both by-products was studied by applying the hydrolates in vitro on seeds and mixing the distillation straws with the growing substrate. Lavandin hydrolates significantly inhibited germination and growth of the four weeds used, being also phytotoxic for monocotyledonous crops, but hardly showed a phytotoxic effect on the dicotyledonous crops (lentil and vetch). With respect to lavandin distilled straws, they had an allelopathic effect of growth inhibition on all weeds and crops used in the work. In both by-products, lysophosphatidylcholine was identified as one of the major metabolites, while coumaroyl hexoside and feruloyl hexoside were identified as major metabolites only present in the straws. So far, only the phytotoxic capacity of the metabolites lysophosphatidylcholine and coumaroyl hexoside had been described. Therefore, by-products from the industrial distillation of lavandin could be used in the development of effective and sustainable bioherbicides, due to the allelopathic capacity of the metabolites present.

A novel mutation Trp-2027-Gly in acetyl-CoA carboxylase confers resistance to cyhalofop-butyl in Chinese sprangletop (Leptochloa chinensis)

BACKGROUND

Chinese sprangletop [Leptochloa chinensis (L.) Nees] control is threatened by resistance to acetyl-CoA carboxylase (ACCase)-inhibiting herbicides. In this study, a L. chinensis population, HFLJ18, that survived cyhalofop-butyl [aryloxyphenoxypropionate (APP) herbicide, CyB] treatment was collected from a rice field in Lujiang County, Anhui Province, China. This study aimed to evaluate the susceptibility of HFLJ18 to herbicides with different modes-of-action and investigate the potential mechanisms of resistance to CyB.

RESULTS

The HFLJ18 population exhibited high levels of resistance to CyB (10.92-fold) and showed resistance to the ACCase inhibitors metamifop (4.63-fold) and fenoxaprop-P-ethyl (8.39-fold), but was susceptible to clethodim, pinoxaden, florpyrauxifen-benzyl, oxadiazon and pretilachlor. Target gene sequencing revealed a novel Trp-to-Gly substitution at codon position 2027 of ACCase in the resistant plants. Molecular docking revealed that the spatial structure of ACCase changed significantly following the substitution, as indicated by reduced H-bonds. A newly derived cleaved amplified polymorphic sequence (dCAPS) marker was subsequently developed to detect the Trp-2027-Gly mutation in the ACCase of L. chinensis. Additionally, pretreatment with the cytochrome P450 (P450) inhibitor piperonyl butoxide (PBO) and the glutathione S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) did not reverse resistance to CyB, suggesting that nontarget-site resistance mechanisms were not involved in CyB resistance in the HFLJ18 population.

CONCLUSION

Overall, the resistance to CyB in the HFLJ18 population derived from the mutation of ACCase gene, and to the best of our knowledge, this is the first report of the ACCase Trp-2027-Gly mutation conferring resistance to ACCase-inhibiting herbicides in grass species. © 2024 Society of Chemical Industry.

Comparison of Molecularly Identified Resistant and Susceptible Johnsongrass (Sorghum halepense L.) Populations at ALS Gene, in the Absence and Presence of Field Crops

BACKGROUND/OBJECTIVES

Johnsongrass (Sorghum halepense) is an erect tetraploid, perennial, C4 grass weed species categorized among the world's most noxious weeds due to its high competitive ability against crops and the increased number of field-evolved herbicide-resistant populations. The aim of the present study was to assess the growth rate and performance of resistant (R) johnsongrass genotypes hosting Trp574Leu target-site cross-resistance at ALS gene, inhibiting various herbicides, compared to susceptible (S) conspecific weeds, in the absence and presence of corn or sunflower antagonism.

METHODS

The aboveground biomass, tiller, and rhizome production ability of one S and one R johnsongrass population with a Trp574-Leu substitution conferring cross-resistance to ALS-inhibiting herbicides were compared under non-competitive conditions. Furthermore, the competitive ability of these two johnsongrass populations against corn or sunflower was determined in a target-neighborhood design.

RESULTS

The S and R johnsongrass populations displayed similar growth rates concerning aboveground biomass and tiller number, whereas the R population displayed a slightly greater growth rate for rhizome production compared to the S population. Both populations grown with corn produced more aboveground biomass than the ones grown with sunflowers. The aboveground biomass of corn was reduced to a greater extent than sunflower by the presence of both johnsongrass populations, while both crops were affected more by the S than by the R population.

CONCLUSIONS

Although the inheritance and the genetic background of plant materls were not addressed, the findings of this study indicate clearly that the growth rate and competitive ability of the ALS-resistant johnsongrass population are not associated with the resistance mechanism involved.

A new amino acid substitution in the MvALS1 gene of metsulfuron-methyl resistant biotypes Monochoria vaginalis (Burm. f.) C. Presl from West Java, Indonesia

The most bothersome weed in rice fields in the Indonesian province of West Java is Monochoria vaginalis (Burm. F.) C. Presl, an aquatic herbaceous plant. Metsulfuron-methyl has long been used in wetland rice in West Java with a high enough intensity. However, the case of Monochoria vaginalis resistance to metsulfuron-methyl herbicides in Indonesia has not been widely reported and investigated. The study aims to (1) classify the resistance level of M. vaginalis toward metsulfuron-methyl, (2) identify Target Site Resistance (TSR) mechanism mutations in the MvALS1 gene of the resistant biotype of M. vaginalis. The Whole Plant Pot Test method was utilized to assess the resistance level of Monochoria vaginalis. Following that, all samples were subjected to DNA sequencing using the PCR method to identify mutations in the MvALS1 gene from the resistant biotype. After then, this study used DUET, a server with an integrated computational methodology, to anticipate the effect of mutations on protein stability. The result showed that Monochoria vaginalis from Rawamerta, Karawang showed a moderate level of resistance to metsulfuron-methyl with a resistance ratio of 6.00, Patokbeusi, Subang showed a low level of resistance to metsulfuron-methyl with a resistance ratio of 3.89, compared to susceptible Monochoria vaginalis. Nucleotide base alignment in the MvALS1 gene revealed that base substitutions occurred in the Monochoria vaginalis biotype from Rawamerta and Patokbeusi, resulting in 5 amino acid substitutions: Ser-64-Ala, Asp-66-Glu, Asn-240-Asp, Glu-426-Asn, and Ser-469-Asn and Sukra: Ser-64-Ala, Asp-66-Glu, and Asn-240-Asp. The analysis showed that S64A, D66E, and N240D stabilize the protein, whereas E426N and S469N destabilize it. This study confirms for the first time that Ser-64-Ala, Asn-240-Asp, and Glu-426-Asn amino acid mutations were found in cases of M. vaginalis resistance to metsulfuron-methyl (ALS inhibitor).

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

N-Phenylnorbornenesuccinimide derivatives, agricultural defensive, and enzymatic target selection

BACKGROUND

Faced with the need to develop new herbicides with modes of action different to those observed for existing agrochemicals, one of the most promising strategies employed by synthetic chemists involves the structural modification of molecules found in natural products. Molecules containing amides, imides, and epoxides as functional groups are prevalent in nature and find extensive application in synthesizing more intricate compounds due to their biological properties. In this context, this paper delineates the synthesis of N-phenylnorbornenesuccinimide derivatives, conducts biological assays, and carries out in silico investigation of the protein target associated with the most potent compound in plant organisms. The phytotoxic effects of the synthesized compounds (2-29) were evaluated on Allium cepa, Bidens pilosa, Cucumis sativus, Sorghum bicolor, and Solanum lycopersicum.

RESULTS

Reaction of endo-bicyclo[2.2.1]hept-5-ene-3a,7a-dicarboxylic anhydride (1) with aromatic amines led to the N-phenylnorbornenesuccinic acids (2-11) with yields ranging from 75% to 90%. Cyclization of compounds (2-11) in the presence of acetic anhydride and sodium acetate afforded N-phenylnorbornenesuccinimides (12-20) with yields varying from 65% to 89%. Those imides were then subjected to epoxidation reaction to afford N-phenylepoxynorbornanesuccimides (21-29) with yields from 60% to 90%. All compounds inhibited the growth of seedlings of the plants evaluated. Substance 23 was the most active against the plants tested, inhibiting 100% the growth of all species in all concentrations. Cyclophilin was found to be the enzymatic target of compound 23.

CONCLUSION

These findings suggest that derivatives of N-phenylnorbornenesuccinimide are promising compounds in the quest for more selective and stable agrochemicals. This perspective reinforces the significance of these derivatives as potential innovative herbicides and emphasizes the importance of further exploring their biological activity on weeds. © 2024 Society of Chemical Industry.

Current status of community resources and priorities for weed genomics research

Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.

Dominance and multi-locus interaction

Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with the genetic background of the focal locus. Here, alleles at other loci modify the observed phenotype through position effects or dominance modifiers that are sometimes associated with pathogen resistance, lineage, sex, or mating type. Theoretical models have illustrated how variable dominance appears in the context of multi-locus interaction (epistasis). Here, we review empirical evidence for variable dominance and how the observed patterns may be captured by proposed epistatic models. We highlight how integrating epistasis and dominance is crucial for comprehensively understanding adaptation and speciation.

Evolutionary plant-pollinator responses to anthropogenic land-use change: impacts on ecosystem services

Agricultural intensification at field and landscape scales, including increased use of agrochemicals and loss of semi-natural habitats, is a major driver of insect declines and other community changes. Efforts to understand and mitigate these effects have traditionally focused on ecological responses. At the same time, adaptations to pesticide use and habitat fragmentation in both insects and flowering plants show the potential for rapid evolution. Yet we lack an understanding of how such evolutionary responses may propagate within and between trophic levels with ensuing consequences for conservation of species and ecological functions in agroecosystems. Here, we review the literature on the consequences of agricultural intensification on plant and animal evolutionary responses and interactions. We present a novel conceptualization of evolutionary change induced by agricultural intensification at field and landscape scales and emphasize direct and indirect effects of rapid evolution on ecosystem services. We exemplify by focusing on economically and ecologically important interactions between plants and pollinators. We showcase available eco-evolutionary theory and plant-pollinator modelling that can improve predictions of how agricultural intensification affects interaction networks, and highlight available genetic and trait-focused methodological approaches. Specifically, we focus on how spatial genetic structure affects the probability of propagated responses, and how the structure of interaction networks modulates effects of evolutionary change in individual species. Thereby, we highlight how combined trait-based eco-evolutionary modelling, functionally explicit quantitative genetics, and genomic analyses may shed light on conditions where evolutionary responses impact important ecosystem services.

Herbicide resistance evolution, fitness cost, and the fear of the superweeds

Despite considerable differences in cropping systems around the globe, chemical weed control is a key tool in conventional agroecosystems, which has led to an increase in herbicide resistance. Although mutations causing resistance are thought to have an adaptation cost in resistant plants compared to the susceptible ones under herbicide-free conditions, such cost may not always express or will express under certain ecological conditions. To ensure that herbicides will keep going as viable instruments in agricultural production, strategies to minimize resistance are needed. Proactive or reactive strategies for weed control should utilize an overall integrated weed management approach by combining as many weed management practices as possible. The term 'superweed' was used initially to describe the phenomenon in which genetically engineered crops would become troublesome weeds and that the genes of interest would spread into related weeds, rendering them problematic, or into wild species, turning them into troublesome weeds. Contrary to the above definition, the use of this term in the literature has often been linked with herbicide resistance, mostly related to the cultivation of genetically engineered crops and the related increase in the use of glyphosate, which rapidly selected resistant weed populations. From a scientific point of view, weeds are better survivors than non-weedy species and cause crop problems because they have several unique traits, e.g., they are aggressive, adapt easily to different environments, produce many seeds, compete strongly with crops, disperse easily, are difficult to control, traits which occur whether weeds are herbicide-resistant or not. We propose that the term 'superweed' should be referred to weeds with resistant populations to several herbicides with diverse modes of action (MOAs).

Intergenerational consequences of an auxin-like herbicide on plant sensitivity to a graminicide mediated by a fungal endophyte

In agroecosystems, herbicides are the predominant anthropogenic selection pressure for agriculture weed species. While weeds are the primary target, herbicides can have adverse impacts on non-target plant beneficial microorganisms. We aimed to investigate the influence of a foliar endophytic fungus (Epichloë occultans) on the sensitivity of Lolium multiflorum to a graminicide herbicide (diclofop-methyl) during both plant ontogeny and progeny. Susceptible individuals to diclofop-methyl with and without endophyte were pre-exposed to the auxin 2,4-D herbicide. This herbicide is known to stimulate the metabolic detoxification mechanism (CYP-450) of diclofop-methyl. Regardless of the endophyte, 2,4-D pre-treatment increased mother plant survival to nearly 100 % under diclofop treatment but not in the progeny. Furthermore, maternal plant exposure to 2,4-D reduced endophyte transmission to the seeds and from seed-to-seedlings. Our findings suggest that, despite a reduction in diclofop-methyl sensitivity during the ontogeny of mother plants, 2,4-D-mediated induction of likely CYP-450 metabolism is not intergenerationally transmitted and shows detrimental effects on the symbiotic endophyte persistence.

Phytotoxic fungal secondary metabolites as herbicides

Among the alternatives to synthetic plant protection products, biocontrol appears as a promising method. This review reports on the diversity of fungal secondary metabolites phytotoxic to weeds and on the approach generally used to extract, characterize, identify and exploit them for weed management. The 183 phytotoxic fungal secondary metabolites discussed in this review fall into five main classes of molecules: 61 polyketides, 53 terpenoids, 36 nitrogenous metabolites, 18 phenols and phenolic acids, and 15 miscellaneous. They are mainly produced by the genera Drechslera, Fusarium and Alternaria. The phytotoxic effects, more often described by the symptoms they produce on plants than by their mode of action, range from inhibition of germination to inhibition of root and vegetative growth, including tissue and organ alterations. The biochemical characterization of fungal secondary metabolites requires expertise and tools to carry out fungal cultivation and metabolite extraction, phytotoxicity tests, purification and fractionation of the extracts, and chemical identification procedures. Phytotoxicity tests are mainly carried out under controlled laboratory conditions (not always on whole plants), while effectiveness against targeted weeds and environmental impacts must be assessed in greenhouses and open fields. These steps are necessary for the formulation of effective, environment-friendly fungal secondary metabolites-derived bioherbicides using new technologies such as nanomaterials. © 2023 Society of Chemical Industry.

Biological lessons for strategic resistance management

Biological resistance to pesticides, vaccines, antibiotics, and chemotherapies creates huge costs to society, including extensive morbidity and mortality. We simultaneously face costly resistance to social changes, such as those required to resolve human-wildlife conflicts and conserve biodiversity and the biosphere. Viewing resistance as a force that impedes change from one state to another, we suggest that an analysis of biological resistance can provide unique and potentially testable insights into understanding resistance to social changes. We review key insights from managing biological resistance and develop a framework that identifies seven strategies to overcome resistance. We apply this framework to consider how it might be used to understand social resistance and generate potentially novel hypotheses that may be useful to both enhance the development of strategies to manage resistance and modulate change in socio-ecological systems.

Phytochemical Cue for the Fitness Costs of Herbicide-Resistant Weeds

Despite increasing knowledge of the fitness costs of viability and fecundity involved in the herbicide-resistant weeds, relatively little is known about the linkage between herbicide resistance costs and phytochemical cues in weed species and biotypes. This study demonstrated relative fitness and phytochemical responses in six herbicide-resistant weeds and their susceptible counterparts. There were significant differences in the parameters of viability (growth and photosynthesis), fecundity fitness (flowering and seed biomass) and a ubiquitous phytochemical (-)-loliolide levels between herbicide-resistant weeds and their susceptible counterparts. Fitness costs occurred in herbicide-resistant Digitaria sanguinalis and Leptochloa chinensis but they were not observed in herbicide-resistant Alopecurus japonicas, Eleusine indica, Ammannia arenaria, and Echinochloa crus-galli. Correlation analysis indicated that the morphological characteristics of resistant and susceptible weeds were negatively correlated with (-)-loliolide concentration, but positively correlated with lipid peroxidation malondialdehyde and total phenol contents. Principal component analysis showed that the lower the (-)-loliolide concentration, the stronger the adaptability in E. crus-galli and E. indica. Therefore, not all herbicide-resistant weeds have fitness costs, but the findings showed several examples of resistance leading to improved fitness even in the absence of herbicides. In particular, (-)-loliolide may act as a phytochemical cue to explain the fitness cost of herbicide-resistant weeds by regulating vitality and fecundity.

Early growth, development and allometry of glyphosate-resistant and susceptible Amaranthus palmeri in response to current and elevated temperature and CO2

This study aimed to evaluate the influence of CO2 and temperature on glyphosate-resistant and susceptible biotypes of Amaranthus palmeri (Palmer amaranth) in terms of morphological development. Height (cm), stem diameter (cm), leaf area (cm2), number of leaves, leaf, stem, and root dry matter, plant volume (m3), as well as shoot-to-root allometry were evaluated. The Palmer amaranth biotypes were grown under four different scenarios: 1-low temperature (23/33 °C) and CO2 (410 ± 25 ppm); 2-low temperature (23/33 °C) and high CO2 (750 ± 25 ppm); 3-high temperature (26/36 °C) and low CO2 (410 ± 25 ppm); and 4-high temperature (26/36 °C) and CO2 (750 ± 25 ppm). Between CO2 and temperature, the majority of differences observed were driven by CO2 levels. Palmer amaranth grown under 750 ppm of CO2 was 15.5% taller, displayed 10% more leaf area (cm2), 18% more stem dry matter, and had a 28.4% increase in volume (m3) compared to 410 ppm of CO2. GA2017 and GA2020 were 18% and 15.5% shorter, respectively. The number of leaves was 27% greater for GA2005. Plant volume decreased in GA2017 (35.6%) and GA2020 (23.8%). The shoot-to-root ratio was isomeric, except at 14 and 21 DAT, where an allometric growth towards shoot development was significant. Palmer amaranth biotypes responded differently to elevated CO2, and the impacts of temperature need further investigation on weed physiology. Thus, environmental and genetic background may affect the response of glyphosate-resistant and susceptible populations to climate change scenarios.

Theoretical assessment of persistence and adaptation in weeds with complex life cycles

Herbicide-resistant weeds pose a substantial threat to global food security. Perennial weed species are particularly troublesome. Such perennials as Sorghum halepense spread quickly and are difficult to manage due to their ability to reproduce sexually via seeds and asexually through rhizomes. Our theoretical study of S. halepense incorporates this complex life cycle with control measures of herbicide application and tillage. Rooted in the biology and experimental data of S. halepense, our population-based model predicts population dynamics and target-site resistance evolution in this perennial weed. We found that the resistance cost determines the standing genetic variation for herbicide resistance. The sexual phase of the life cycle, including self-pollination and seed bank dynamics, contributes substantially to the persistence and rapid adaptation of S. halepense. While self-pollination accelerates target-site resistance evolution, seed banks considerably increase the probability of escape from control strategies and maintain genetic variation. Combining tillage and herbicide application effectively reduces weed densities and the risk of control failure without delaying resistance adaptation. We also show how mixtures of different herbicide classes are superior to rotations and mono-treatment in controlling perennial weeds and resistance evolution. Thus, by integrating experimental data and agronomic views, our theoretical study synergistically contributes to understanding and tackling the global threat to food security from resistant weeds.

Barnyard Grass Stress Triggers Changes in Root Traits and Phytohormone Levels in Allelopathic and Non-Allelopathic Rice

Despite the growing knowledge concerning allelopathic interference with barnyard grass, little is understood regarding the competitive physiological mechanisms of the interaction between allelopathic rice and herbicide-resistant barnyard grass. A hydroponic system was employed to investigate the root morphological traits and different phytohormonal changes in allelopathic and non-allelopathic rice cultivars when co-planted with quinclorac-resistant and -susceptible barnyard grass, respectively. The results show that shoot and root biomass were greater in PI. Barnyard grass stress induced an increase in shoot and root biomass in PI at 7 and 14 days of co-culturing rice and barnyard grass. Especially under the stress of quinclorac-resistant barnyard grass, the shoot biomass of PI increased by 23% and 68%, respectively, and the root biomass increased by 37% and 34%, respectively. In terms of root morphology, PI exhibited a significantly higher fine-root length, in root diameters of <0.5 mm, a greater number of root tips, and longer root tips compared to LE. The response to quinclorac-resistant barnyard grass stress was consistent in terms of the SA and JA content. The obvious accumulation of SA and JA was observed in two rice cultivars under quinclorac-resistant barnyard grass stress, with greater amounts of SA and JA in PI. The significant decrease in auxin (IAA) and abscisic acid (ABA) content in rice was detected from 7 to 14 days under co-culture stress. Additionally, highly significant and positive correlations were found between SA and JA content, and the number of root tips and root tip length at root diameters of 0-0.5 mm in rice.

Molecular basis of two pyrimidine-sulfonylurea herbicides: from supramolecular arrangement to acetolactate synthase inhibition

CONTEXT

The design and synthesis of safe and highly active sulfonylurea herbicides is still a challenge. Therefore, following some principles of structure-activity relationship (SAR) of sulfonylurea herbicides, this work focuses on evaluating two sulfonylurea derivatives bearing electron-withdrawing substituents, namely, -(CO)OCH₃ and -NO₂ on the aryl group, on herbicidal activity. To understand the effects caused by the substituent groups, the molecular and electronic structures of the sulfonylureas were evaluated by density functional theory. Likewise, the crystalline supramolecular arrangements of both compounds were analyzed by Hirshfeld surface, QTAIM, and NBO, with the aim of verifying changes in intermolecular interactions caused by substituent groups. Finally, through a toxicophoric analysis, we were able to predict the interacting groups in their biological target, acetolactate synthase, and verify the interactions with the binding site.

METHODS

All theoretical calculations were conducted using the highly parameterized empirical exchange-correlation functional M06-2X accompanied by the diffuse and polarized basis set 6-311++G(d,p). The atomic coordinates were obtained directly from the crystalline structures, and from the energies of the frontier molecular orbitals (HOMO and LUMO), chemical descriptors were obtained that indicated the influence of the functional groups in the sulfonylureas on the reactivity of the molecules. The intermolecular interactions in the crystals were analyzed using the Hirshfeld, QTAIM, and NBO surfaces. Toxicophoric modeling was performed by the PharmaGist webserver and molecular docking calculations were performed by the GOLD 2022.1.0 software package so that the ligand was fitted to the binding site in a 10 Å sphere. For this, genetic algorithm parameters were used using the ChemPLP scoring function for docking and ASP for redocking.

The consequences of synthetic auxin herbicide on plant-herbivore interactions

Although herbicide drift is a common side effect of herbicide application in agroecosystems, its effects on the ecology and evolution of natural communities are rarely studied. A recent shift to dicamba, a synthetic auxin herbicide known for 'drifting' to nontarget areas, necessitates the examination of drift effects on the plant-insect interactions that drive eco-evo dynamics in weed communities. We review current knowledge of direct effects of synthetic auxin herbicides on plant-insect interactions, focusing on plant herbivory, and discuss potential indirect effects, which are cascading effects on organisms that interact with herbicide-exposed plants. We end by developing a framework for the study of plant-insect interactions given drift, highlighting potential changes to plant developmental timing, resource quantity, quality, and cues.

Roundup and immune challenge have different effects on a native field cricket and its introduced competitor

Animals face many natural challenges, and humans have added to this burden by applying potentially harmful herbicides and unintentionally introducing competitors. We examine the recently introduced Velarifictorus micado Japanese burrowing cricket which shares the same microhabitat and mating season as the native Gryllus pennsylvanicus field cricket. In this study, we assess the combined effects of Roundup (glyphosate-based herbicide) and a lipopolysaccharide (LPS) immune challenge on both crickets. In both species, an immune challenge reduced the numbers of eggs that the female laid; however, this effect was much larger in G. pennsylvanicus. Conversely, Roundup caused both species to increase egg production, potentially representing a terminal investment strategy. When exposed to both an immune challenge and herbicide, G. pennsylvanicus fecundity was harmed more than V. micado fecundity. Furthermore, V. micado females laid significantly more eggs than G. pennsylvanicus, suggesting that introduced V. micado may have a competitive edge in fecundity over native G. pennsylvanicus. LPS and Roundup each had differing effects on male G. pennsylvanicus and V. micado calling effort. Overall, introduced male V. micado spent significantly more time calling than native G. pennsylvanicus, which could potentially facilitate the spread of this introduced species. Despite the population-level spread of introduced V. micado, in our study, this species did not outperform native G. pennsylvanicus in tolerating immune and chemical challenge. Although V. micado appears to possess traits that make this introduced species successful in colonizing new habitats, it may be less successful in traits that would allow it to outcompete a native species.

New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae)

BACKGROUND

While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa.

RESULTS

Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported.

CONCLUSIONS

The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.

Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.

Kin Recognition in an Herbicide-Resistant Barnyardgrass (Echinochloa crus-galli L.) Biotype

Despite increasing evidence of kin recognition in natural and crop plants, there is a lack of knowledge of kin recognition in herbicide-resistant weeds that are escalating in cropping systems. Here, we identified a penoxsulam-resistant barnyardgrass biotype with the ability for kin recognition from two biotypes of penoxsulam-susceptible barnyardgrass and normal barnyardgrass at different levels of relatedness. When grown with closely related penoxsulam-susceptible barnyardgrass, penoxsulam-resistant barnyardgrass reduced root growth and distribution, lowering belowground competition, and advanced flowering and increased seed production, enhancing reproductive effectiveness. However, such kin recognition responses were not occurred in the presence of distantly related normal barnyardgrass. Root segregation, soil activated carbon amendment, and root exudates incubation indicated chemically-mediated kin recognition among barnyardgrass biotypes. Interestingly, penoxsulam-resistant barnyardgrass significantly reduced a putative signaling (-)-loliolide production in the presence of closely related biotype but increased production when growing with distantly related biotype and more distantly related interspecific allelopathic rice cultivar. Importantly, genetically identical penoxsulam-resistant and -susceptible barnyardgrass biotypes synergistically interact to influence the action of allelopathic rice cultivar. Therefore, kin recognition in plants could also occur at the herbicide-resistant barnyardgrass biotype level, and intraspecific kin recognition may facilitate cooperation between genetically related biotypes to compete with interspecific rice, offering many potential implications and applications in paddy systems.

Biochemical analysis, photosynthetic gene (psbA) down–regulation, and in silico receptor prediction in weeds in response to exogenous application of phenolic acids and their analogs

Chemical herbicides are the primary weed management tool, although several incidences of herbicide resistance have emerged, causing serious threat to agricultural sustainability. Plant derived phenolic acids with herbicidal potential provide organic and eco-friendly substitute to such harmful chemicals. In present study, phytotoxicity of two phenolic compounds, ferulic acid (FA) and gallic acid (GA), was evaluated in vitro and in vivo against three prevalent herbicide-resistant weed species (Sinapis arvensis, Lolium multiflorum and Parthenium hysterophorus). FA and GA not only suppressed the weed germination (80 to 60% respectively), but also negatively affected biochemical and photosynthetic pathway of weeds. In addition to significantly lowering the total protein and chlorophyll contents of the targeted weed species, the application of FA and GA treatments increased levels of antioxidant enzymes and lipid peroxidation. Photosynthetic gene (psbA) expression was downregulated (10 to 30 folds) post 48 h of phenolic application. In silico analysis for receptor identification of FA and GA in psbA protein (D1) showed histidine (his-198) and threonine (thr-286) as novel receptors of FA and GA. These two receptors differ from the D1 amino acid receptors which have previously been identified (serine-264 and histidine-215) in response to PSII inhibitor herbicides. Based on its toxicity responses, structural analogs of FA were also designed. Four out of twelve analogs (0.25 mM) significantly inhibited weed germination (30 to 40%) while enhancing their oxidative stress. These results are unique which provide fundamental evidence of phytotoxicity of FA and GA and their analogs to develop cutting-edge plant based bio-herbicides formulation in future.

Evaluation of Propiophenone, 4-Methylacetophenone and 2',4'-Dimethylacetophenone as Phytotoxic Compounds of Labdanum Oil from Cistus ladanifer L

This is the first study to evaluate the phytotoxic activity of three phenolic compounds present in the essential oil of the labdanum of Cistus ladanifer, an allelopathic species of the Mediterranean ecosystem. Propiophenone, 4'-methylacetophenone, and 2',4'-dimethylacetophenone slightly inhibit total germination and radicle growth of Lactuca sativa, and they strongly delay germination and reduce hypocotyl size. On the other hand, the inhibition effect of these compounds on Allium cepa was stronger on total germination than on germination rate, and radicle length compared to hypocotyl size. The position and number of methyl groups will affect the efficacy of the derivative. 2',4'-dimethylacetophenone was the most phytotoxic compound. The activity of the compounds depended on their concentration and presented hormetic effects. In L. sativa, on paper, propiophenone presented greater inhibition of hypocotyl size at greater concentrations, with IC₅₀ = 0.1 mM, whereas 4'-methylacetophenone obtained IC₅₀ = 0.4 mM for germination rate. When the mixture of the three compounds was applied, in L. sativa, on paper, the inhibition effect on total germination and the germination rate was significantly greater compared to the effect of the compounds when they were applied separately; moreover, the mixture inhibited radicle growth, whereas propiophenone and 4'-methylacetophenone did not exert such effect when applied separately. The activity of the pure compounds and that of the mixture also changed based on the substrate used. When the trial was conducted in soil, the separate compounds delayed the germination of the A. cepa to a greater extent compared to the trial on paper, although they stimulated seedling growth. In soil, L. sativa against 4'-methylacetophenone also showed the opposite effect at low concentrations (0.1 mM), with stimulation of germination rate, whereas propiophenone and 4'-methylacetophenone presented a slightly increased effect.

Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds

Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop-wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre-adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super-crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well-domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed-control practices and breeding better crops. © 2022 Society of Chemical Industry.

The blackgrass genome reveals patterns of non-parallel evolution of polygenic herbicide resistance

Globally, weedy plants are a major constraint to sustainable crop production. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated management of agroecosystems. Alopecurus myosuroides (blackgrass) is a widespread and impactful weed affecting agriculture in Europe. Here we report a chromosome-scale genome assembly of blackgrass and use this reference genome to explore the genomic/genetic basis of non-target site herbicide resistance (NTSR). Based on our analysis of F2 seed families derived from two distinct blackgrass populations with the same NTSR phenotype, we demonstrate that the trait is polygenic and evolves from standing genetic variation. We present evidence that selection for NTSR has signatures of both parallel and non-parallel evolution. There are parallel and non-parallel changes at the transcriptional level of several stress- and defence-responsive gene families. At the genomic level, however, the genetic loci underpinning NTSR are different (non-parallel) between seed families. We speculate that variation in the number, regulation and function of stress- and defence-related gene families enable weedy species to rapidly evolve NTSR via exaptation of genes within large multi-functional gene families. These results provide novel insights into the potential for, and nature of plant adaptation in rapidly changing environments.

Interspecific variation in resistance and tolerance to herbicide drift reveals potential consequences for plant community co-flowering interactions and structure at the agro-eco interface

BACKGROUND AND AIMS

When plant communities are exposed to herbicide 'drift', wherein particles containing the active ingredient travel off-target, interspecific variation in resistance or tolerance may scale up to affect community dynamics. In turn, these alterations could threaten the diversity and stability of agro-ecosystems. We investigated the effects of herbicide drift on the growth and reproduction of 25 wild plant species to make predictions about the consequences of drift exposure on plant-plant interactions and the broader ecological community.

METHODS

We exposed potted plants from species that commonly occur in agricultural areas to a drift-level dose of the widely used herbicide dicamba or a control solution in the glasshouse. We evaluated species-level variation in resistance and tolerance for vegetative and floral traits. We assessed community-level impacts of drift by comparing the species evenness and flowering networks of glasshouse synthetic communities comprised of drift-exposed and control plants.

KEY RESULTS

Species varied significantly in resistance and tolerance to dicamba drift: some were negatively impacted while others showed overcompensatory responses. Species also differed in the way they deployed flowers over time following drift exposure. While drift had negligible effects on community evenness based on vegetative biomass, it caused salient differences in the structure of co-flowering networks within communities. Drift reduced the degree and intensity of flowering overlap among species, altered the composition of groups of species that were more likely to co-flower with each other than with others and shifted species roles (e.g. from dominant to inferior floral producers, and vice versa).

CONCLUSIONS

These results demonstrate that even low levels of herbicide exposure can significantly alter plant growth and reproduction, particularly flowering phenology. If field-grown plants respond similarly, then these changes would probably impact plant-plant competitive dynamics and potentially plant-pollinator interactions occurring within plant communities at the agro-ecological interface.

Evolution of weedy giant ragweed (Ambrosia trifida): Multiple origins and gene expression variability facilitates weediness

Agricultural weeds may originate from wild populations, but the origination patterns and genetics underlying this transition remain largely unknown. Analysis of weedy-wild paired populations from independent locations may provide evidence to identify key genetic variation contributing to this adaptive shift. We performed genetic variation and expression analyses on transcriptome data from 67 giant ragweed samples collected from different locations in Ohio, Iowa, and Minnesota and found geographically separated weedy populations likely originated independently from their adjacent wild populations, but subsequent spreading of weedy populations also occurred locally. By using eight closely related weedy-wild paired populations, we identified thousands of unique transcripts in weedy populations that reflect shared or specific functions corresponding, respectively, to both convergently evolved and population-specific weediness processes. In addition, differential expression of specific groups of genes was detected between weedy and wild giant ragweed populations using gene expression diversity and gene co-expression network analyses. Our study suggests an integrated route of weedy giant ragweed origination, consisting of independent origination combined with the subsequent spreading of certain weedy populations, and provides several lines of evidence to support the hypothesis that gene expression variability plays a key role in the evolution of weedy species.

Herbicidal characteristics and structural identification of a potential active compound produced by Streptomyces sp. KRA18-249

The KRA18-249 strain, isolated from a natural recreational forest near Jeongseon, Gangwon-do, when applied to plants induced signs of wilting within 24 h, leading to plant death. The isolated actinomycete was identified as Streptomyces gardneri based on 16S rRNA gene homogeneity analysis. The culture filtrate was solvent fractionated to obtain the active substance, and the active compound 249-Y1 was isolated from the purified fractions via a herbicide activity test using Digitaria ciliaris. NMR and ESI-MS analyses revealed that the molecular formula of 249-Y1 is C₂₀H₁₆O₆ [MW = 352.0947] and is an anthraquinone (rubiginone D2) produce by polyketide synthetase system. The active compound 249-Y1 showed strong (100%) herbicidal activity against several weeds at 500 μg mL^-1 concentration. Twisting symptoms began to appear within 24 h of treatment and intensified over time. The KRA18-249 strain produced the herbicidal compound under specific culture conditions, that is, at 200 rpm, 35 °C, for eight days at an initial pH of 10. We also found that 249-Y1 inhibited chlorophyll, but was not a radical generator. Overall, the secondary metabolite 249-Y1, produced by KRA18-249, can be used as a new biological agent for weed control.

Dissecting weed adaptation: Fitness and trait correlations in herbicide-resistant Alopecurus myosuroides

BACKGROUND

Unravelling the genetic architecture of non-target-site resistance (NTSR) traits in weed populations can inform questions about the inheritance, trade-offs and fitness costs associated with these traits. Classical quantitative genetics approaches allow study of the genetic architecture of polygenic traits even where the genetic basis of adaptation remains unknown. These approaches have the potential to overcome some of the limitations of previous studies into the genetics and fitness of NTSR.

RESULTS

Using a quantitative genetic analysis of 400 pedigreed Alopecurus myosuroides seed families from nine field-collected populations, we found strong heritability for resistance to the acetolactate synthase and acetyl CoA carboxylase inhibitors (h²  = 0.731 and 0.938, respectively), and evidence for shared additive genetic variance for resistance to these two different herbicide modes of action, r_g  = 0.34 (survival), 0.38 (biomass). We find no evidence for genetic correlations between life-history traits and herbicide resistance, indicating that resistance to these two modes of action is not associated with large fitness costs in blackgrass. We do, however, demonstrate that phenotypic variation in plant flowering characteristics is heritable, h²  = 0.213 (flower height), 0.529 (flower head number), 0.449 (time to flowering) and 0.372 (time to seed shed), demonstrating the potential for adaptation to other nonchemical management practices (e.g. mowing of flowering heads) now being adopted for blackgrass control.

CONCLUSION

These results highlight that quantitative genetics can provide important insight into the inheritance and genetic architecture of NTSR, and can be used alongside emerging molecular techniques to better understand the evolutionary and fitness landscape of herbicide resistance. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Resistance to ALS inhibitors conferred by non-target-site resistance mechanisms in Myosoton aquaticum L

Myosoton aquaticum L. is a competitive broadleaf weed commonly found in wheat fields in China and has become challenging due to its evolving herbicide resistance. In this study, one subpopulation, RF1 (derived from the tribenuron-methyl-resistant population HN10), with none of the known acetolactate synthase (ALS) resistance mutations was confirmed to exhibit resistance to tribenuron-methyl (SU), pyrithiobac‑sodium (PTB), florasulam (TP), flucarbazone-Na (SCT), and diflufenican (PDS). In vitro ALS activity assays showed that the total ALS activity of RF1 was lower than that of the susceptible (S) population. However, there was no difference in ALS gene expression induced by tribenuron-methyl between the two populations. The combination of the cytochrome P450 monooxygenase (P450) inhibitor malathion and tribenuron-methyl resulted in the RF1 population behaving like the S population. The rapid P450-mediated tribenuron-methyl metabolism in RF1 plants was also confirmed by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. In addition, approximately equal glutathione S-transferase (GST) activity was observed in RF1 and S plants of untreated and tribenuron-methyl treated groups. This study reported one M. aquaticum L. population without ALS resistance mutations exhibiting resistance to ALS inhibitors and the PDS inhibitor diflufenican, and the non-target-site resistance mechanism played a vital role in herbicide resistance.

Potential Risks of Microplastic Fomites to Aquatic Organisms with Special Emphasis on Polyethylene-Microplastic-Glyphosate Exposure Case in Aquacultured Shrimp

Plastic litter is increasingly becoming pervasive in aquatic environments, characterized by circulatory patterns between different compartments and continual loading with new debris. Microplastic pollution can cause a variety of effects on aquatic organisms. This review presents the current knowledge of microplastics distribution and sorption capacity, reflecting on possible bioaccumulation and health effects in aquatic organisms. A model case study reveals the fate and toxic effects of glyphosate, focusing on the simultaneous exposure of aquacultured shrimp to polyethylene and glyphosate and their contact route and on the potential effects on their health and the risk for transmission of the contaminants. The toxicity and bioaccumulation of glyphosate-sorbed polyethylene microplastics in shrimp are not well understood, although individual effects have been studied extensively in various organisms. We aim to delineate this knowledge gap by compiling current information regarding the co-exposure to polyethylene microplastic adsorbed with glyphosate to assist in the assessment of the possible health risks to aquacultured shrimp and their consumers.

Global drivers of herbicide-resistant weed richness in major cereal crops worldwide

BACKGROUND

The number of herbicide-resistant weeds differs across the globe but the reasons for this variation are poorly understood. Taking a macroecological approach, the role of six drivers of herbicide resistance in a country was examined for barley, maize, rice and wheat crops worldwide. Drivers captured agronomic measures (crop harvested area, herbicide and fertilizer input) as well as sources of sampling bias that result in under-reporting of herbicide resistance (human population density, research intensity and time since the first record of resistance).

RESULTS

Depending on the crop, best subset regression models explained between 60% and 80% of the variation in herbicide-resistant weeds recorded in countries worldwide. Global prevalence of herbicide-resistant weeds is likely underestimated, especially in countries with limited capability in herbicide research. Numbers of resistant weeds worldwide will continue to increase. Agricultural intensification, captured by fertilizer and herbicide input, as well as further expansion of crop harvested area are primary drivers of future herbicide-resistant weeds.

CONCLUSION

Because the evolution of herbicide resistance lags behind the selection pressures imposed by fertilizer and herbicide inputs, several countries (e.g. Brazil, South Africa, Uruguay) appear to exhibit a 'herbicide resistance debt' in which current agronomic conditions have set the scene for higher numbers of herbicide-resistant weeds than currently observed. Future agricultural expansion will lead to more herbicide-resistant weeds, especially in developing countries as their economies grow and where herbicide resistance is currently under-reported. A global strategy for increasing national capability in herbicide resistance research is needed. © 2022 The Author. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

CYP81A68 confers metabolic resistance to ALS and ACCase-inhibiting herbicides and its epigenetic regulation in Echinochloa crus-galli

Long-term and excessive herbicide use has led to some environmental concerns and especially, herbicide resistance evolution in weeds. Here, we confirmed acetolactate synthase (ALS) inhibiting herbicide penoxsulam resistance and cross resistance to acetyl-coenzyme carboxylase (ACCase) inhibiting herbicides (cyhalofop-butyl and metamifop) in a global weed Echinochloa crus-galli population resistant to these herbicides (R). Penoxsulam metabolism study indicated that degradation rate was significantly higher in R than susceptible E. crus-galli population (S). RNA-sequencing revealed that a cytochrome P450 (P450) gene, CYP81A68, expressed higher in R versus S. Rice seedlings overexpressing this CYP81A68 gene are resistant to penoxsulam, cyhalofop-butyl and metamifop, and penoxsulam resistance is due to enhanced metabolism via O-demethylation. Deletion analysis of the CYP81A68 gene promoter identified an efficient region, in which differential methylation of CpG islands occurred between R and S. Collectively, these results demonstrate that upregulation of E. crus-galli CYP81A68 gene endows generalist metabolic resistance to commonly used ALS- and ACCase-inhibiting herbicides in rice fields and epigenetic regulation may play a role in the resistance evolution. This research could contribute to strategies reducing herbicide environmental impacts by judicious selection of alternative herbicide and non-chemical control tactics.

A dinitroaniline herbicide resistance mutation can be nearly lethal to plants

BACKGROUND

Lolium rigidum is the most important weed in Australian agriculture and pre-emergence dinitroaniline herbicides (e.g., trifluralin) are widely and persistently used for Lolium control. Consequently, evolution of resistance to dinitroaniline herbicides has been increasingly reported. Resistance-endowing target-site α-tubulin gene mutations are identified with varying frequency. This study investigated the putative fitness cost associated with the common resistance mutation Val-202-Phe and the rare resistance mutation Arg-243-Met causing helical plant growth.

RESULTS

Results showed a deleterious effect of Arg-243-Met on fitness when plants are homozygous for this mutation. This was evidenced as high plant mortality, severely diminished root and aboveground vegetative growth (lower relative growth rate), and very poor fecundity compared with the wild-type, which led to a nearly lethal fitness cost of >99.9% in competition with a wheat crop. A fitness penalty in vegetative growth was evident, but to a much lesser extent, in plants heterozygous for the Arg-243-Met mutation. By contrast, plants possessing the Val-202-Phe mutation exhibited a fitness advantage in vegetative and reproductive growth.

CONCLUSION

The α-tubulin mutations Arg-243-Met and Val-202-Phe have contrasting effects on fitness. These results help understand the absence of plants homozygous for the Arg-243-Met mutation and the high frequency of plants carrying the Val-202-Phe mutation in dinitroaniline-resistant L. rigidum populations. The α-tubulin Arg-243-Met mutation can have an exceptional fitness cost with nearly lethal effects on resistant L. rigidum plants. © 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.

Acetolactate Synthase-Inhibitor Resistance in Monochoria vaginalis (Burm. f.) C. Presl from Indonesia

Monochoria vaginalis (Burm. f.) C. Presl, belonging to the family Pontederiaceae, is an aquatic herbaceous plant, native to temperate and tropical Asia. The species often occurs in paddy fields as a noxious weed in East Asia, and in the USA, and causes a significant reduction in rice production. The objective of the present research was the evaluation of the resistance levels of M. vaginalis against three chemical groups of acetolactate synthase (ALS)-inhibitor herbicides and other two different groups of herbicides, and the investigation of the mutations in the ALS gene of the resistant biotype of M. vaginalis. Herbicide dose-response experiments showed that the resistant biotype of M. vaginalis was highly resistant to bensulfuron-methyl, moderately resistant to bispyribac-sodium, had low resistance to penoxsulam and 2,4-D dimethyl ammonium, and was susceptible to sulfentrazone. The nucleotide sequences of the ALS gene of resistant and susceptible biotypes showed 14 base substitutions, which caused two amino acid substitutions: Val-143-Ile and Val-148-Ile. It is the first report of the substitutions of amino acids Val-143-Ile and Val-148-Ile in ALS protein. Those mutations may give different resistance spectra against three ALS-inhibitor herbicides: bensulfuron-methyl, bispyribac-sodium, and penoxsulam. Further research is needed to elucidate the molecular basis of target-site resistance mechanisms such as the transformation of the ALS gene of M. vaginalis. It is also necessary to evaluate herbicide mixtures and/or the rotation of herbicide sites of action to control the resistant biotype of M. vaginalis.