Investigating the Mechanism of Metabolic Resistance to Tribenuron-Methyl in Capsella bursa-pastoris (L.) Medik. by Full-Length Transcriptome Assembly Combined with RNA-Seq

Physiological Basis for the Mechanism of Selectivity of Tripyrasulfone between Rice (Oryza sativa) and Barnyard Grass (Echinochloa crus-galli)

Tripyrasulfone is currently the only HPPD-inhibiting herbicide that possesses outstanding selectivity even for direct-seeded rice (Oryza sativa) when applied POST to control grass weeds; however, the underlying mechanisms remain unclear. In this study, the inhibitory effects of the real active HDT of tripyrasulfone on recombinant 4-hydroxyphenylpyruvate dioxygenase (HPPDs) from rice and barnyard grass (Echinochloa crus-galli) were similar, with consistent structural interactions and similar binding energies predicted by molecular docking. However, the HPPD expression level in rice was significantly greater than that in barnyard grass after tripyrasulfone treatment. Tripyrasulfone was rapidly taken up and hydrolyzed into HDT, which was similarly distributed within the whole plants of rice and barnyard grass at 24 h after treatment. Compared with barnyard grass, rice has more uniform epicuticular wax in the cuticle of its leaves, absorbing less tripyrasulfone and metabolizing much more tripyrasulfone. Overall, to a greater extent, the different sensitivities to tripyrasulfone between barnyard grass and rice resulted from metabolic variations.

Metabolism-Based Herbicide Resistance to Mesosulfuron-methyl and Identification of Candidate Genes in Bromus japonicus

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.

Epigenetic Regulation of CYP72A385-Mediated Metabolic Resistance to Novel Auxin Herbicide Florpyrauxifen-benzyl in Echinochloa crus-galli (L.) P. Beauv

Weed's metabolic resistance to herbicides has undermined the sustainability of herbicides and global food security. Notably, we identified an Echinochloa crus-galli (L.) P. Beauv population (R) that evolved resistance to the never-used florpyrauxifen-benzyl, in which florpyrauxifen-benzyl was metabolized faster than the susceptible E. crus-galli population (S). RNA-seq identified potential metabolism-related genes, EcCYP72A385 and EcCYP85A1, whose expression in yeast exhibited the capacity to degrade florpyrauxifen-benzyl. Region-2 in the EcCYP72A385 promoter showed significant demethylation after florpyrauxifen-benzyl treatment in the R population. DNA methyltransferase inhibitors induce EcCYP72A385 overexpression in the S population and endow it with tolerance to florpyrauxifen-benzyl. Moreover, methyltransferase-like 7A (EcMETTL7A) was overexpressed in the S population and specifically bound to the EcCYP72A385 promoter. Transgenic EcCYP72A385 in Arabidopsis and Oryza sativa L. exhibited resistance to florpyrauxifen-benzyl, whereas EcMETTL7A transgenic plants were sensitive. Overall, EcCYP72A385 is the principal functional gene for conferring resistance to florpyrauxifen-benzyl and is regulated by EcMETTL7A in E. crus-galli.

Weed biology and management in the multi-omics era: Progress and perspectives

Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.

Diverse ALS mutations and cross-and multiple-resistance to ALS and EPSPS inhibitors in flucarbazone‑sodium-resistant Bromus japonicus populations from Hebei province, China

Japanese brome (Bromus japonicus) has become one of the main weeds in wheat fields in Hebei province of China and causes a large decrease of wheat production. A total of 44 putative resistant and 2 susceptible Japanese brome populations were collected in the 2021/2022 crop season from Hebei province of China to determine resistance levels to flucarbazone‑sodium and to investigate the diversity of acetolactate synthase (ALS) mutations, as well as to confirm the cross-and multiple-resistance levels to ALS and EPSPS (5-enolpyruvate shikimate-3-phosphate synthetase) inhibitors. Whole plant bioassay results showed that 15 out of 44 populations tested or 34% were resistant to flucarbazone‑sodium. The resistance indices of Japanese brome to flucarbazone‑sodium ranged from 43 to 1977. The resistant populations were mainly distributed in Baoding and Shijiazhuang districts, and there was only one resistant population in Langfang district. Resistant Japanese brome had diverse ALS mutations, including Pro-197-Ser, -Thr, -Arg and Asp-376-Glu. The incidence of Pro-197-Ser mutation was the highest at 68%. Application of the CYP450 inhibitor malathion suggested that CYP450 was involved in metabolic resistance in a population without an ALS mutation. The population with Pro-197-Thr mutation evolved weak cross-resistance to mesosulfuron-methyl and pyroxsulam, and it is in the process of evolving multiple-resistance to glyphosate.

Postmortem Muscle Proteome Characteristics of Silver Carp (Hypophthalmichthys molitrix): Insights from Full-Length Transcriptome and Deep 4D Label-Free Proteomic

The coverage of the protein database directly determines the results of shotgun proteomics. In this study, PacBio single-molecule real-time sequencing technology was performed on postmortem silver carp muscle transcripts. A total of 42.43 Gb clean data, 35,834 nonredundant transcripts, and 15,413 unigenes were obtained. In total, 99.32% of the unigenes were successfully annotated and assigned specific functions. PacBio long-read isoform sequencing (Iso-Seq) analysis can provide more accurate protein information with a higher proportion of complete coding sequences and longer lengths. Subsequently, 2671 proteins were identified in deep 4D proteomics informed by a full-length transcriptomics technique, which has been shown to improve the identification of low-abundance muscle proteins and potential protein isoforms. The feature of the sarcomeric protein profile and information on more than 30 major proteins in the white dorsal muscle of silver carp were reported here for the first time. Overall, this study provides valuable transcriptome data resources and the comprehensive muscle protein information detected to date for further study into the processing characteristic of early postmortem fish muscle, as well as a spectral library for data-independent acquisition and data processing. This batch of muscle-specific dependent acquisition data is available via PRIDE with identifier PXD043702.

Distinctive physiological and molecular responses of foxtail millet and maize to nicosulfuron

Introduction

Nicosulfuron is the leading acetolactate synthase inhibitor herbicide product, and widely used to control gramineous weeds. Here, we investigated the metabolic process of nicosulfuron into foxtail millet and maize, in order to clarify the mechanism of the difference in sensitivity of foxtail millet and maize to nicosulfuron from the perspective of physiological metabolism and provide a theoretical basis for the breeding of nicosulfuron-resistant foxtail millet varieties.

Methods

We treated foxtail millet (Zhangzagu 10, Jingu 21) and maize (Nongda 108, Ditian 8) with various doses of nicosulfuron in both pot and field experiments. The malonaldehyde (MDA) content, target enzymes, detoxification enzymes, and antioxidant enzymes, as well as related gene expression levels in the leaf tissues of foxtail millet and maize were measured, and the yield was determined after maturity.

Results

The results showed that the recommended dose of nicosulfuron caused Zhangzagu 10 and Jingu 21 to fail to harvest; the yield of the sensitive maize variety (Ditian 8) decreased by 37.09%, whereas that of the resistant maize variety (Nongda 108) did not decrease. Nicosulfuron stress increased the CYP450 enzyme activity, MDA content, and antioxidant enzyme activity of foxtail millet and maize, reduced the acetolactate synthase (ALS) activity and ALS gene expression of foxtail millet and Ditian 8, and reduced the glutathione S-transferase (GST) activity and GST gene expression of foxtail millet. In conclusion, target enzymes, detoxification enzymes, and antioxidant enzymes were involved in the detoxification metabolism of nicosulfuron in plants. ALS and GST are the main factors responsible for the metabolic differences among foxtail millet, sensitive maize varieties, and resistant maize varieties.

Discussion

These findings offer valuable insights for exploring the target resistance (TSR) and non-target resistance (NTSR) mechanisms in foxtail millet under herbicide stress and provides theoretical basis for future research of develop foxtail millet germplasm with diverse herbicide resistance traits.

Enhanced metabolic resistance mechanism endows resistance to metamifop in Echinochloa crus-galli (L.) P. Beauv

Barnyardgrass (Echinochloa crus-galli (L.) P. Beauv.), one of the worst weeds in paddy fields in China, has been frequently reported evolving resistance to acetyl-CoA carboxylase (ACCase) inhibiting herbicides. However, in the previous research, more attention was paid to target-site resistance (TSR) mechanisms, the non-target-site resistance (NTSR) mechanisms have not been well-established. In this study, the potential mechanism of resistance in a metamifop-resistant E. crus-galli collected from Kunshan city, Jiangsu Province, China was investigated. Dose-response assays showed that the phenotypic resistant population (JS-R) has evolved 4.3-fold resistance to metamifop compared with the phenotypic susceptible population (YN-S). The ACCase CT gene sequencing and relative ACCase gene expression levels studies showed that no mutations were detected in the ACCase CT gene in both YN-S and JS-R, and there was no significant difference in the relative ACCase gene expression between YN-S and JS-R. After the pre-processing of glutathione-S-transferase (GSTs) inhibitor NBD-Cl, the resistance level of JS-R to metamifop was reversed 18.73%. Furthermore, the GSTs activity of JS-R plants was significantly enhanced compared to that of YN-S plants. UPLC-MS/MS revealed that JS-R plants had faster metabolic rates to metamifop than YN-S plants. Meanwhile, the JS-R popultion exhibited resistant to cyhalofop-butyl and penoxsulam. In summary, this study presented a novel discovery regarding the global emergence of metabolic resistance to metamifop in E. crus-galli. The low-level resistance observed in the JS-R population was not found to be related to TSR but rather appeared to be primarily associated with the overexpression of genes in the GSTs metabolic enzyme superfamily.

Detoxification mechanism of herbicide in Polypogon fugax and its influence on rhizosphere enzyme activities

The excessive use of chemical herbicides has resulted in evolution of herbicide-resistant weeds. Cytochrome P450 monooxygenases (P450s) are vital detoxification enzymes for herbicide-resistant weeds. Herein, we confirmed a resistant (R) Polypogon fugax population showing resistance to quizalofop-p-ethyl, acetolactate synthase (ALS)-inhibiting herbicide pyroxsulam, and several other ACCase (acetyl-CoA carboxylase)-inhibiting herbicides. Molecular analysis revealed no target-site gene mutations in the R population. Foliar spraying with malathion clearly reversed the quizalofop-p-ethyl phytotoxicity. Higher level of quizalofop-p-ethyl degradation was confirmed in the R population using HPLC analysis. Subsequently, RNA-Seq transcriptome analysis indicated that the overexpression of CYP89A2 gene appeared to be responsible for reducing quizalofop-p-ethyl phytotoxicity. The molecular docking results supported a metabolic effect of CYP89A2 protein on most herbicides tested. Furthermore, we found that low doses of herbicides stimulated the rhizosphere enzyme activities in P. fugax and the increase of rhizosphere dehydrogenase of R population may be related to its resistance mechanism. In summary, our research has shown that metabolic herbicide resistance mediated by CYP89A2, contributes to quizalofop-p-ethyl resistance in P. fugax.

Investigating the Metabolic Mesosulfuron-Methyl Resistance in Aegilops tauschii Coss. By Transcriptome Sequencing Combined with the Reference Genome

Aegilops tauschii Coss. is a malignant weed in wheat fields in China, its herbicide resistance has been threatening crop production. This study identified one mesosulfuron-methyl-resistant(R) population, JJMHN2018-05 (R), without target resistance mutations. To fully understand the resistance mechanism, non-target site resistance was investigated by using transcriptome sequencing combined with a reference genome. Results showed that the cytochrome P450 monooxygenase (P450) inhibitor malathion significantly increased the mesosulfuron-methyl sensitivity in R plants, and greater herbicide-induced glutathione S-transferase (GST) activity was also confirmed. Liquid chromatography with tandem mass spectrometry analysis further supported the enhanced mesosulfuron-methyl metabolism in R plants. Gene expression data analysis and qRT-PCR validation indicated that eight P450s, six GSTs, two glycosyltransferases (GTs), four peroxidases, and one aldo-keto reductase (AKRs) stably upregulated in R plants. This research demonstrates that the P450s and GSTs involved in enhanced mesosulfuron-methyl metabolism contribute to mesosulfuron-methyl resistance in A. tauschii and identifies potential contributors from metabolic enzyme families.

Pro-197-Ser Mutation and Cytochrome P450-Mediated Metabolism Conferring Resistance to Flucarbazone-Sodium in Bromus japonicus

In crop fields, resistance to acetolactate synthase (ALS)-inhibiting herbicides found in many troublesome weed species, including Bromus japonicus Thunb, is a worldwide problem. In particular, the development of herbicide resistance in B. japonicus is a severe threat to wheat production in China. The purpose of this research was to investigate the physiological and molecular basis of B. japonicus resistance to flucarbazone-sodium. Dose-response analysis demonstrated that, compared with the susceptible B. japonicus (S) population, the resistant (R) population exhibited a 120-fold increase in flucarbazone-sodium resistance. Nucleotide sequence alignment of the ALS gene indicated that the Pro-197-Ser mutation in ALS was associated with resistance to flucarbazone-sodium in the R population. The results of a malathion pretreatment study showed that B. japonicus might also have remarkable cytochrome P450 monooxygenase (P450)-mediated metabolic resistance. This is the first report of a Pro-197-Ser mutation and P450-mediated metabolism conferring resistance to flucarbazone-sodium in B. japonicus.

The Metabolism of a Novel Cytochrome P450 (CYP77B34) in Tribenuron-Methyl-Resistant Descurainia sophia L. to Herbicides with Different Mode of Actions

Descurainia sophia L. (flixweeds) is a noxious broad-leaf weed infesting winter wheat fields in China that has evolved high resistance to tribenuron-methyl. In this work, a brand new gene CYP77B34 was cloned from tribenuron-methyl-resistant (TR) D. sophia and transferred into Arabidopsis thaliana, and the sensitivities of Arabidopsis with or without the CYP77B34 transgene to herbicides with a different mode of actions (MoAs) were tested. Compared to Arabidopsis expressing pCAMBIA1302-GFP (empty plasmid), Arabidopsis transferring pCAMBIA1302-CYP77B34 (recombinant plasmid) became resistant to acetolactate synthase (ALS)-inhibiting herbicide tribenuron-methyl, protoporphyrinogen oxidase (PPO)-inhibiting herbicides carfentrazone-ethyl and oxyfluorfen. Cytochrome P450 inhibitor malathion could reverse the resistance to tribenuron-methyl, carfentrazone-ethyl and oxyfluorfen in transgenic Arabidopsis plants. In addition, the metabolic rates of tribenuron-methyl in Arabidopsis expressing CYP77B34 were significantly higher than those in Arabidopsis expressing pCAMBIA1302-GFP. Other than that, the transgenic plants showed some tolerance to very-long-chain fatty acid synthesis (VLCFAs)-inhibiting herbicide pretilachlor and photosystem (PS) II-inhibiting herbicide bromoxynil. Subcellular localization revealed that the CYP77B34 protein was located in the endoplasmic reticulum (ER). These results clearly indicated that CYP77B34 mediated D. sophia resistance to tribenuron-methyl and may have been involved in D. sophia cross-resistance to carfentrazone-ethyl, oxyfluorfen, pretilachlor and bromoxynil.

Identification of essential genes involved in metabolism-based resistance mechanism to fenoxaprop-P-ethyl in Polypogon fugax

BACKGROUND

Metabolic resistance is a worldwide concern for weed control but has not yet been well-characterized at the genetic level. Previously, we have identified an Asia minor bluegrass (Polypogon fugax Nees ex Steud.) population AHHY exhibiting cytochrome P450 (P450)-involved metabolic resistance to fenoxaprop-P-ethyl. In this study, we aimed to confirm the metabolic fenoxaprop-P-ethyl resistance in AHHY and uncover the potential herbicide metabolism-related genes in this economically damaging weed species.

RESULTS

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays indicated the metabolic rates of fenoxaprop-P-ethyl were significantly faster in resistant (R, AHHY) than in susceptible (S, SDTS) plants. The amount of phytotoxic fenoxaprop-P peaked at 12 h after herbicide treatment (HAT) and started to decrease at 24 HAT in both biotypes. R and S plants at 24 HAT were sampled to conduct isoform-sequencing (Iso-Seq) and RNA-sequencing (RNA-Seq). A reference transcriptome containing 24 972 full-length isoforms was obtained, of which 24 329 unigenes were successfully annotated. Transcriptomic profiling identified 28 detoxifying enzyme genes constitutively and/or herbicide-induced up-regulated in R than in S plants. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed 17 genes were consistently up-regulated in R and its F1 generation plants. They were selected as potential fenoxaprop-P-ethyl metabolism-related genes, including ten P450s, one glutathione-S-transferase, one UDP-glucosyltransferase, and five adenosine triphosphate (ATP)-binding cassette transporters.

CONCLUSION

This study revealed that the enhanced rates of fenoxaprop-P-ethyl metabolism in P. fugax were very likely driven by the herbicide metabolism-related genes. The transcriptome data generated by Iso-Seq combined with RNA-Seq will provide abundant gene resources for understanding the molecular mechanisms of resistance in P. fugax.