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Mechanisms of Herbicide Resistance in Weeds
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Mechanisms of Herbicide Resistance in Weeds

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 5850

Special Issue Editors

Dr. Hailan Cui

E-Mail Website
Guest Editor
Institute of Plant Protection, Chinese Academy of Agricultural Sciences; Beijing 100193, China
Interests: weed; herbicide resistance; weed management; weed biology and ecology; molecular resistance mechanism of weeds in crop fields; early and rapid detection of resistant weeds in farmland
Dr. Jingchao Chen

E-Mail Website
Guest Editor
Institute of Plant Protection, Chinese Academy of Agricultural Sciences; Beijing 100193, China
Interests: weed; herbicide resistance; mechanisms of weed resistance to non-selective herbicides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Weeds are a kind of biotic threat to agricultural production, causing crop yield losses and health hazards, and impairing product quality. Herbicides are one of the most effective ways to control weeds; however, relying heavily on herbicides results in the development of resistance. To clarify the mechanism of weed resistance to herbicides, it is very important to develop a rapid resistance detection method in order to decide on a strategy for weed control. Many scientific studies have been carried out to understand herbicide resistance and have been shared with the public. However, more knowledge on herbicide resistance is still needed, especially using genomics, transcriptomics, and other omics techniques, as well as monitoring measures and control strategies of resistant weeds that depend on clear resistance mechanisms.

The aim and scope of this Special Issue, titled “Mechanisms of Herbicide Resistance in Weeds”, are to elucidate the biochemical and molecular resistance mechanisms of weeds to herbicides, especially using omics techniques and novel weed control strategies that have never been reported. Topics of interest include, but are not limited to, the following:

  • Target-site/non-target-site herbicide resistance;
  • Molecular basis of evolution in herbicide resistance;
  • Fitness traits of herbicide-resistant weeds;
  • Omics techniques in weeds;
  • Rapid methods for detection of herbicide resistance in weeds;
  • Management of herbicide/stress resistance.

We welcome novel research articles and reviews addressing all related topics.

Dr. Hailan Cui
Dr. Jingchao Chen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • weeds
  • herbicide resistance
  • resistance mechanisms to herbicides
  • omics technique
  • weed management

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Published Papers (7 papers)

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Research

16 pages, 3933 KiB  
Article
Resistance to Amino Acid Biosynthesis Inhibiting-Herbicides in Amaranthus palmeri Populations from Aragon (Spain)
by Eneko Trebol-Aizpurua, Mikel V. Eceiza, Clara Jimenez-Martinez, Ana I. Marí, Mercedes Royuela, Ana Zabalza and Miriam Gil-Monreal
Plants 2025, 14(10), 1505; https://doi.org/10.3390/plants14101505 - 17 May 2025
Viewed by 152
Abstract
Amaranthus palmeri is a highly problematic agricultural weed due to its rapid growth, high seed production, and strong tendency to develop herbicide resistance. In Spain, the initial colonization of A. palmeri began in 2007, when populations were detected at various locations in the [...] Read more.
Amaranthus palmeri is a highly problematic agricultural weed due to its rapid growth, high seed production, and strong tendency to develop herbicide resistance. In Spain, the initial colonization of A. palmeri began in 2007, when populations were detected at various locations in the province of Lleida (Catalonia). Since then, new infestations have been reported in other regions of the country, primarily infesting maize fields. Although resistance to glyphosate or to acetolactate synthase (ALS) inhibitors has been documented in several populations from Catalonia and Extremadura, little is known about the resistance profile of populations from Aragon. The main objective of this study was to characterize the putative resistance of five populations from Aragon to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) inhibitors (glyphosate) and ALS inhibitors (nicosulfuron and imazamox). Sensitivity to both mechanisms of action was measured by root growth in vertical plates and shikimate accumulation for glyphosate. Target-site resistance was evaluated by analyzing EPSPS and ALS gene copy numbers and ALS gene mutations. The populations showed high variability, with no multiple resistance detected. The Bujaraloz population showed moderate resistance to glyphosate due to EPSPS gene amplification. In three populations, mutations in the ALS gene conferring resistance were detected. The Trp574Leu mutation was detected in approximately half of the individuals from the Albelda, Tamarite de Litera, and Caspe populations. In the latter, the Pro197Thr mutation was also present. This study reveals significant genetic variability within each population and provides evidence for the spread of herbicide resistance across different regions of Spain. Full article
(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)
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16 pages, 7885 KiB  
Article
Niches and Genotypes Determine the Diversity and Composition of Microbiomes After Herbicide Treatment in Beckmannia syzigachne
by Kehan Bai, Yulan Ouyang, Jiale Qi, You Zhan and Junzhi Wang
Plants 2025, 14(6), 876; https://doi.org/10.3390/plants14060876 - 11 Mar 2025
Viewed by 614
Abstract
Plant-associated microbes play a crucial role in plant adaptability by facilitating nutrient acquisition, growth, and stress resistance. However, the effects of herbicides on microbial communities in different root-associated niches and their impact on weed–microbe interactions are not well understood. Beckmannia syzigachne, a [...] Read more.
Plant-associated microbes play a crucial role in plant adaptability by facilitating nutrient acquisition, growth, and stress resistance. However, the effects of herbicides on microbial communities in different root-associated niches and their impact on weed–microbe interactions are not well understood. Beckmannia syzigachne, a problematic weed, reduces crop yield and quality. In this study, we investigated bacterial and fungal community diversity in B. syzigachne using 16S and internal transcribed spacer (ITS) rRNA sequencing. Significant differences were observed in bacterial community structure across four root-associated niches, with diversity decreasing from bulk soil to endosphere. The sensitive genotype exhibited higher bacterial diversity compared to the resistant biotype, indicating that sample type is the primary factor influencing microbial community composition, with genotype playing a secondary role. Additionally, we examined fungal communities in sensitive and resistant populations, identifying 271 fungal operational taxonomic units (OTUs). Ascomycota, Basidiomycota, and Rozellomycota were dominant in the sensitive population, while the resistant population contained two unique OTUs, Saccharomyces sp. and Apiotrichum montevideense, which were absent in the sensitive population. This study provides insights into how bacterial and fungal communities in B. syzigachne populations respond to herbicide exposure, contributing to a deeper understanding of weed–microbe interactions. Full article
(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)
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10 pages, 1448 KiB  
Communication
Effect of Different Temperatures on Herbicide Efficacy for the Management of the Invasive Weed Solanum rostratum Dunal (Family: Solanaceae)
by Jackline Abu-Nassar and Maor Matzrafi
Plants 2025, 14(4), 574; https://doi.org/10.3390/plants14040574 - 13 Feb 2025
Viewed by 587
Abstract
Solanum rostratum Dunal, an invasive weed first recorded in Israel in the 1950s, undergoes multiple germination waves from early spring to late summer. Recently, its distribution has significantly expanded, with new populations reported throughout the country. This study assessed the efficacy of various [...] Read more.
Solanum rostratum Dunal, an invasive weed first recorded in Israel in the 1950s, undergoes multiple germination waves from early spring to late summer. Recently, its distribution has significantly expanded, with new populations reported throughout the country. This study assessed the efficacy of various herbicides for controlling S. rostratum populations under two distinct temperature regimes, focusing on temperature-dependent variations in herbicide performance. The results demonstrated that fluroxypyr and tembotrione consistently achieved high levels of control across all temperature conditions. Conversely, oxyfluorfen exhibited low performance under elevated temperatures and showed greater population-specific variability, while metribuzin proved more effective at higher temperatures across all S. rostratum populations. These findings emphasize the pivotal role of post-application temperature in influencing herbicide efficacy and underscore the importance of a precise application timing to optimize the control outcomes. Temperature-optimized herbicide strategies could play a critical role in limiting the spread and establishment of S. rostratum in agricultural systems, contributing to a sustainable and effective weed management. Full article
(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)
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15 pages, 8460 KiB  
Article
Rapid Resistance Detection of Amaranthus retroflexus to Fomesafen via Kompetitive Allele-Specific PCR (KASP)
by Zhanzhan Zhang, Yaxin Ban, Jianguo Wei, Qun Wu, Liyao Dong and Zhike Feng
Plants 2025, 14(4), 515; https://doi.org/10.3390/plants14040515 - 8 Feb 2025
Viewed by 661
Abstract
Amaranthus retroflexus is a highly invasive annual broadleaf weed in soybean fields, significantly reducing soybean yield and quality. Diphenyl ether herbicides, particularly fomesafen, are extensively applied to control A. retroflexus. Fomesafen resistance of A. retroflexus is emerging in Northeast China, and rapid [...] Read more.
Amaranthus retroflexus is a highly invasive annual broadleaf weed in soybean fields, significantly reducing soybean yield and quality. Diphenyl ether herbicides, particularly fomesafen, are extensively applied to control A. retroflexus. Fomesafen resistance of A. retroflexus is emerging in Northeast China, and rapid resistance detection is urgent for managing these resistant weeds. An Arg-128-Gly mutation in the ppo2 gene of A. retroflexus has been shown to confer fomesafen resistance. In current study, we developed a rapid detection method based on Kompetitive Allele-Specific PCR (KASP) technology to detect the Arg-128-Gly mutation in the ppo2 gene of A. retroflexus. Initially, we developed this KASP detection method using cDNA as the template; however, the entire process requires significant costs and considerable operational time. To mitigate these expenses and simplify the workflow, we subsequently optimized this KASP rapid detection method by utilizing genomic DNA as the template. This new resistance detection technique directly utilizes A. retroflexus genomic DNA as the template, and, by adding specific labelled primers, probes, and enzymes, it can determine whether the ppo2 gene harbors an Arg-128-Gly mutation, thereby rapidly identifying fomesafen resistance in A. retroflexus. Furthermore, we compared the detection efficiency of the new KASP assay, whole plant dose–response assay, and DNA sequencing, all of which produced consistent outcomes, supporting the accuracy and reliability of the KASP rapid detection method. Collectively, we established a rapid resistance detection method based on KASP technology, which is of high reliability and time-saving, and will significantly advance precise management of resistant weeds. Full article
(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)
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13 pages, 1738 KiB  
Article
Affecting of Glyphosate Tolerance and Metabolite Content in Transgenic Arabidopsis thaliana Overexpressing EPSPS Gene from Eleusine indica
by Jingchao Chen, Zhiling Li, Haiyan Yu, Hailan Cui and Xiangju Li
Plants 2025, 14(1), 78; https://doi.org/10.3390/plants14010078 - 30 Dec 2024
Cited by 1 | Viewed by 830
Abstract
Long-term use of the global non-selective herbicide glyphosate for weed control has caused resistance in weeds. Overproducing of the target of glyphosate 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is one of the resistance mechanisms in weeds. However, few studies have measured the effects on tolerance levels [...] Read more.
Long-term use of the global non-selective herbicide glyphosate for weed control has caused resistance in weeds. Overproducing of the target of glyphosate 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is one of the resistance mechanisms in weeds. However, few studies have measured the effects on tolerance levels and metabolite content in model plant species overexpressing EPSPS from weeds. We assessed the resistance levels of transgenic Arabidopsis thaliana overexpressing EPSPS from Eleusine indica, and its effects on metabolite content using the method of both quasi-targeted and targeted metabolomics. The results showed that the average resistance index of the transgenic lines was 4.7 and the exogenous E. indica EPSPS expression levels were 265.3- to 532.0-fold higher than those in the wild-type (WT) line. The EPSPS protein ranged from 148.5 to 286.2 μg g−1, which was substantially higher than that in the WT line (9.1 μg g−1). 103 metabolites associated with flavone and flavonol biosynthesis, the metabolism of aromatic amino acids, energy metabolism, and auxin synthesis were significantly higher in the transgenic glyphosate-resistant individuals (R) than in the WT individuals. The results of quantitative analysis show that pyruvate, sedoheptulose 7-phosphate, and gluconic acid amounts in R plants were 1.1-, 1.6- and 1.3-fold higher than those in WT plants, respectively. However, both citric and glyceric acid levels were 0.9-fold lower than those in WT plants. The abundance of other metabolites in the glycolytic and pentose phosphate pathways of central carbon metabolism was similar in the WT and transgenic plants. Glutamic acid was significantly more abundant in the transgenic line than in the WT plants. In contrast, asparagine, glutamine, and lysine were less abundant. However, the concentration of other amino acids did not change significantly. Overexpression of E. indica EPSPS in A. thaliana conferred a moderate level of tolerance to glyphosate. Metabolites associated with flavone and flavonol biosynthesis, the metabolism of aromatic amino acids, and energy metabolism were significantly increased. The results of this study will be useful for evaluating the characterisation and risk assessment of transgenic plants, including identification of unintended effects of the respective transgenic modifications. Full article
(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)
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12 pages, 1945 KiB  
Article
Pyroxsulam Resistance in Apera spica-venti: An Emerging Challenge in Crop Protection
by Soham Bhattacharya, Madhab Kumar Sen, Katerina Hamouzová, Pavlína Košnarová, Rohit Bharati, Julio Menendez and Josef Soukup
Plants 2025, 14(1), 74; https://doi.org/10.3390/plants14010074 - 29 Dec 2024
Viewed by 884
Abstract
Apera spica-venti, a prevalent weed in Czech winter wheat fields, has developed resistance to ALS-inhibiting herbicides due to their frequent use. This study reports a biotype of A. spica-venti resistant to pyroxsulam, with cross and multiple resistance to iodosulfuron, propoxycarbazone, pinoxaden, and [...] Read more.
Apera spica-venti, a prevalent weed in Czech winter wheat fields, has developed resistance to ALS-inhibiting herbicides due to their frequent use. This study reports a biotype of A. spica-venti resistant to pyroxsulam, with cross and multiple resistance to iodosulfuron, propoxycarbazone, pinoxaden, and chlortoluron. Dose–response experiments revealed high resistance of both R1 and R2 biotypes to pyroxsulam, with resistance factors (RF) of 6.69 and 141.65, respectively. Pre-treatment with malathion reduced RF by 2.40× and 1.25× in R1 and R2, indicating the potential involvement of cytochrome P450 (CytP450). NBD-Cl pre-treatment decreased RF only in R2, suggesting possible GST involvement. Gene analysis revealed no mutations (at previously reported sites) or overexpression in the acetolactate synthase (ALS) gene. However, a significant difference in ALS enzyme activity between resistant and susceptible biotypes points to target-site resistance mechanisms. Studies with 14C-labeled pyroxsulam showed that reduced absorption and translocation were not likely resistance mechanisms. In summary, herbicide resistance in A. spica-venti appears to result from multiple mechanisms. Possible causes include target-site resistance from an unidentified ALS mutation (within coding or regulatory regions). Enhanced herbicide metabolism via CytP450s and GSTs is also a contributing factor. Further experimental validation is needed to confirm these mechanisms and fully understand the resistance. This evolution underscores the adaptive capacity of weed populations under herbicide pressure, emphasizing the need for alternative control strategies. Full article
(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)
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15 pages, 2518 KiB  
Article
Metabolism-Based Herbicide Resistance to Mesosulfuron-methyl and Identification of Candidate Genes in Bromus japonicus
by Qi Li, Hengzhi Wang, Jinping Yu, Wei Zhang, Wenlei Guo and Yixue Liu
Plants 2024, 13(13), 1751; https://doi.org/10.3390/plants13131751 - 25 Jun 2024
Cited by 1 | Viewed by 1442
Abstract
The evolved resistance of Bromus japonicus Houtt. to ALS-inhibiting herbicides is well established. Previous studies have primarily focused on target-site resistance; however, non-target-site resistance has not been well characterized. This investigation demonstrated that ALS gene sequencing did not detect any previously known resistance [...] Read more.
The evolved resistance of Bromus japonicus Houtt. to ALS-inhibiting herbicides is well established. Previous studies have primarily focused on target-site resistance; however, non-target-site resistance has not been well characterized. This investigation demonstrated that ALS gene sequencing did not detect any previously known resistance mutations in a mesosulfuron-methyl-resistant (MR) population, and notably, treatment with the P450 monooxygenase (P450) inhibitor malathion markedly heightened susceptibility to mesosulfuron-methyl. Utilizing UPLC-MS/MS analysis confirmed elevated mesosulfuron-methyl metabolism in MR plants. The integration of Isoform Sequencing (Iso-Seq) and RNA Sequencing (RNA-Seq) facilitated the identification of candidate genes associated with non-target sites in a subpopulation with two generations of herbicide selection. Through qRT-PCR analysis, 21 differentially expressed genes were characterized, and among these, 10 genes (comprising three P450s, two glutathione S-transferases, one glycosyltransferase, two ATP-binding cassette transporters, one oxidase, and one hydrolase) exhibited constitutive upregulation in resistant plants. Our findings substantiated that increased herbicide metabolism is a driving force behind mesosulfuron-methyl resistance in this B. japonicus population. Full article
(This article belongs to the Special Issue Mechanisms of Herbicide Resistance in Weeds)
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