RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum

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.

Genome-wide study of glutathione transferases and their regulation in flufenacet susceptible and resistant black-grass (Alopecurus myosuroides Huds.)

BACKGROUND

Glutathione transferases (GSTs) are enzymes with a wide range of functions, including herbicide detoxification. Up-regulation of GSTs and their detoxification activity enables the grass weed black-grass (Alopecurus myosuroides Huds.) to metabolize the very-long-chain fatty acid synthesis inhibitor flufenacet and other herbicides leading to multiple herbicide resistance. However, the genomic organization and regulation of GSTs genes is still poorly understood.

RESULTS

In this genome-wide study the location and expression of 115 GSTs were investigated using a recently published black-grass genome. Particularly, the most abundant GSTs of class tau and phi were typically clustered and often followed similar expression patterns but possessed divergent upstream regulatory regions. Similarities were found in the promoters of the most up-regulated GSTs, which are located next to each other in a cluster. The binding motif of the E2F/DP transcription factor complex in the promoter of an up-regulated GST was identical in susceptible and resistant plants, however, adjacent sequences differed. This led to a stronger binding of proteins to the motif of the susceptible plant, indicating repressor activity.

CONCLUSIONS

This study constitutes the first analysis dealing with the genomic investigation of GST genes found in black-grass and their transcriptional regulation. It highlights the complexity of the evolution of GSTs in black-grass, their duplication and divergence over time. The large number of GSTs allows weeds to detoxify a broad spectrum of herbicides. Ultimately, more research is needed to fully elucidate the regulatory mechanisms of GST expression. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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.

Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil

An in-depth genotypic characterisation of a diverse collection of Digitaria insularis was undertaken to explore the neutral genetic variation across the natural expansion range of this weed species in Brazil. With the exception of Minas Gerais, populations from all other states showed high estimates of expected heterozygosity (HE > 0.60) and genetic diversity. There was a lack of population structure based on geographic origin and a low population differentiation between populations across the landscape as evidenced by average Fst value of 0.02. On combining haloxyfop [acetyl CoA carboxylase (ACCase)-inhibiting herbicide] efficacy data with neutral genetic variation, we found evidence of presence of two scenarios of resistance evolution in this weed species. Whilst populations originating from north-eastern region demonstrated an active role of gene flow, populations from the mid-western region displayed multiple, independent resistance evolution as the major evolutionary mechanism. A target-site mutation (Trp2027Cys) in the ACCase gene, observed in less than 1% of resistant populations, could not explain the reduced sensitivity of 15% of the populations to haloxyfop. The genetic architecture of resistance to ACCase-inhibiting herbicides was dissected using a genome wide association study (GWAS) approach. GWAS revealed association of three SNPs with reduced sensitivity to haloxyfop and clethodim. In silico analysis of these SNPs revealed important non-target site genes belonging to families involved in herbicide detoxification, including UDPGT91C1 and GT2, and genes involved in vacuolar sequestration-based degradation pathway. Exploration of five genomic prediction models revealed that the highest prediction power (≥0.80) was achieved with the models Bayes A and RKHS, incorporating SNPs with additive effects and epistatic interactions, respectively.

A glutathione S-transferase and a cytochrome P450 may confer cyhalofop-butyl resistance in Leptochloa chinensis (L.) Nees

BACKGROUND

Leptochloa chinensis (L.) Nees is a troublesome weed across China in rice fields, and a suspected L. chinensis resistant population (R) that has survived the recommended field dose of cyhalofop-butyl was collected in a rice field of Hunan Province, China. In this study, we aimed to determine the acetyl-CoA carboxylase-inhibiting herbicide resistance profile of this R population and to investigate its mechanisms of resistance to cyhalofop-butyl.

RESULTS

Compared with the susceptible population (S), the R population was confirmed to be 18.9-, 3.2-, 4.1-, 3.6- and 5.8- fold resistant to the APP herbicides cyhalofop-butyl, haloxyfop-P-methyl, clodinafop-propargyl, metamifop and fenoxaprop-P-ethyl, respectively. ACCase gene sequencing analysis revealed no known resistance mutations for TSR in the R population. Pretreatment with the glutathione S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) and cytochrome P450 (CYP450) inhibitor malathion reversed resistance to cyhalofop-butyl. The GST gene GSTU1 and CYP450 gene CYP707A5 were constitutively upregulated in the R population according to RNA-seq analysis and RT-qPCR verification. The molecular docking results indicated a good affinity of the active site for five APP herbicides with GSTU1 and CYP707A5.

CONCLUSION

This study shows that the GSTU1 and CYP707A5 genes expressed highly in the R population may be responsible for cyhalofop-butyl resistance in L. chinensis.

A high diversity of non-target site resistance mechanisms to acetolactate-synthase (ALS) inhibiting herbicides has evolved within and among field populations of common ragweed (Ambrosia artemisiifolia L.)

BACKGROUND

Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify NTSR genes. However, this approach had generally been applied to a single weed population, limiting our insight into the diversity of NTSR mechanisms. Here, we sought to explore the diversity of NTSR mechanisms in common ragweed (Ambrosia artemisiifolia L.) by investigating six field populations from different French regions where NTSR to acetolactate-synthase-inhibiting herbicides had evolved.

RESULTS

A de novo transcriptome assembly (51,242 contigs, 80.2% completeness) was generated as a reference to seek genes differentially expressed between sensitive and resistant plants from the six populations. Overall, 4,609 constitutively differentially expressed genes were identified, of which none were common to all populations, and only 197 were shared by several populations. Similarly, population-specific transcriptomic response was observed when investigating early herbicide response. Gene ontology enrichment analysis highlighted the involvement of stress response and regulatory pathways, before and after treatment. The expression of 121 candidate constitutive NTSR genes including CYP71, CYP72, CYP94, oxidoreductase, ABC transporters, gluco and glycosyltransferases was measured in 220 phenotyped plants. Differential expression was validated in at least one ragweed population for 28 candidate genes. We investigated whether expression patterns at some combinations of candidate genes could predict phenotype. Within populations, prediction accuracy decreased when applied to an additional, independent plant sampling. Overall, a wide variety of genes linked to NTSR was identified within and among ragweed populations, of which only a subset was captured in our experiments.

CONCLUSION

Our results highlight the complexity and the diversity of NTSR mechanisms that can evolve in a weed species in response to herbicide selective pressure. They strongly point to a non-redundant, population-specific evolution of NTSR to ALS inhibitors in ragweed. It also alerts on the potential of common ragweed for rapid adaptation to drastic environmental or human-driven selective pressures.

Assessment of ACC and P450 Genes Expression in Wild Oat (Avena ludoviciana) in Different Tissues Under Herbicide Application

Target-site resistance (TSR) and non-target-site resistance (NTSR) to herbicides in arable weeds are increasing rapidly all over the world and threatening universal food safety. Resistance to herbicides that inhibit ACCase activity has been identified in wild oat. In this study, expression of ACC1, ACC2, CYP71R4 and CYP81B1 genes under herbicide stress conditions were studied in two TSR (resistant in the residue Ile1781-Leu and Ile2041-Asn of ACCase) biotypes, two NTSR biotypes and one susceptible biotype of A. ludoviciana for the first time. Treated and untreated biotypes with ACCase-inhibitor clodinafop propargyl herbicide were sampled from the stem and leaf tissues at 24 h after treatment. Our results showed an increase in gene expression levels in different tissues of both types of resistance biotypes that occurred under herbicide treatment compared with non-herbicide treatment. In all samples, the expression levels of leaf tissue in all studied genes were higher than in stem tissue. The results of ACC gene expression showed that the expression level of ACC1 was significantly higher than that of ACC2. Also, expression levels of TSR biotypes were higher than NTSR biotypes for the ACC1 gene. For both CYP71R4 and CYP81B1 genes, the expression ratio increased significantly in TSR and NTSR biotypes in different tissues after herbicide treatment. In contrast, the expression levels of CYP genes in NTSR biotypes were higher than in TSR biotypes. Our results support the hypothesis that the reaction of plants to herbicide is carried out through a different regulation of genes, which can be the result of the interaction of resistance type in the target or non-target-site.

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.

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.

Transcriptomic analysis of Amaranthus retroflex resistant to PPO-inhibitory herbicides

Amaranthus retroflexus L. is one of the malignant weeds which can cause a reduction in the soybean yield. We found a population of A. retroflexus (R-Q) resistant to fomesafen through the initial screening of whole-plant dose response bioassay in the research. The resistance index of the population (R-Q) was 183 times of the sensitive population (S-N). The resistant and sensitive populations were used as experimental materials in the paper. Strand-specific RNA-Seq analyses of R‒Q and S‒N populations obtained from herbicide-treated and mock-treated leaf samples after treatment were conducted to generate a full-length transcriptome database. We analyzed differentially expressed genes (DEGs) among the R-Q and S‒N A. retroflexus populations treated with recommended dose and mock-treated on the 1st (24 h) and 3rd (72 h) days to identify genes involved in fomesafen resistance. All 82,287 unigenes were annotated by Blastx search with E-value < 0.00001 from 7 databases. A total of 94,815 DEGs among the three group comparisons were identified. Two nuclear genes encoding PPO (PPX1 and PPX2) and five unigenes belonging to the AP2-EREBP, GRAS, NAC, bHLH and bZIP families exhibited different expression patterns between individuals of S‒N and R-Q populations. The A. retroflexus transcriptome and specific transcription factor families which can respond to fomesafen in resistant and susceptible genotypes were reported in this paper. The PPX1 and PPX2 genes of the target enzyme were identified. The study establishes the foundation for future research and provides opportunities to manage resistant weeds better.

Metabolic resistance to acetolactate synthase inhibitors in Beckmannia syzigachne: identification of CYP81Q32 and its transcription regulation

Frequent herbicide use selects for herbicide resistance in weeds. Cytochrome P450s are important detoxification enzymes responsible for herbicide resistance in plants. We identified and characterized a candidate P450 gene (BsCYP81Q32) from the problematic weed Beckmannia syzigachne to test whether it conferred metabolic resistance to the acetolactate synthase-inhibiting herbicides mesosulfuron-methyl, bispyribac-sodium, and pyriminobac-methyl. Transgenic rice overexpressing BsCYP81Q32 was resistant to the three herbicides. Equally, rice overexpressing the rice ortholog gene OsCYP81Q32 was more resistant to mesosulfuron-methyl. Conversely, an OsCYP81Q32 gene knockout generated using CRISPR/Cas9 enhanced mesosulfuron-methyl sensitivity in rice. Overexpression of the BsCYP81Q32 gene resulted in enhanced mesosulfuron-methyl metabolism in transgenic rice seedlings via O-demethylation. The major metabolite, demethylated mesosulfuron-methyl, was chemically synthesized and displayed reduced herbicidal effect in plants. Moreover, a transcription factor (BsTGAL6) was identified and shown to bind a key region in the BsCYP81Q32 promoter for gene activation. Inhibition of BsTGAL6 expression by salicylic acid treatment in B. syzigachne plants reduced BsCYP81Q32 expression and consequently changed the whole plant response to mesosulfuron-methyl. Sequence polymorphisms in an important region of the BsTGAL6 promoter may explain the higher expression of BsTGAL6 in resistant versus susceptible B. syzigachne plants. Collectively, the present study reveals the evolution of an herbicide-metabolizing and resistance-endowing P450 and its transcription regulation in an economically important weedy plant species.

Transcriptome analysis indicates the involvement of herbicide-responsive and plant-pathogen interaction pathways in the development of resistance to ACCase inhibitors in Apera spica-venti

BACKGROUND

The continuous use of the herbicides contributes to the emergence of the resistant populations of numerous weed species that are tolerant to multiple herbicides with different modes of action (multiple resistance) which is provided by non-target-site resistance mechanisms. In this study, we addressed the question of rapid acquisition of herbicide resistance to pinoxaden (acetyl CoA carboxylase inhibitor) in Apera spica-venti, which endangers winter cereal crops and has high adaptation capabilities to inhabit many rural locations. To this end, de novo transcriptome of Apera spica-venti was assembled and RNA-sequencing analysis of plants resistant and susceptible to pinoxaden treated with this herbicide was performed.

RESULTS

The obtained data showed that the prime candidate genes responsible for herbicide resistance were those encoding 3-ketoacyl-CoA synthase 12-like, UDP-glycosyltransferases (UGT) including UGT75K6, UGT75E2, UGT83A1-like, and glutathione S-transferases (GSTs) such as GSTU1 and GSTU6. Also, such highly accelerated herbicide resistance emergence may result from the enhanced constitutive expression of a wide range of genes involved in detoxification already before herbicide treatment and may also influence response to biotic stresses, which was assumed by the detection of expression changes in genes encoding defence-related proteins, including receptor kinase-like Xa21. Moreover, alterations in the expression of genes associated with methylation in non-treated herbicide-resistant populations were identified.

CONCLUSION

The obtained results indicated genes that may be involved in herbicide resistance. Moreover, they provide valuable insight into the possible effect of resistance on the weed interaction with the other stresses by indicating pathways associated with both abiotic and biotic stresses. © 2023 Society of Chemical Industry.

Transcriptome changes in chlorsulfuron-treated plants are caused by acetolactate synthase inhibition and not induction of a herbicide detoxification system in Marchantia polymorpha

A sensing mechanism in mammals perceives xenobiotics and induces the transcription of genes encoding proteins that detoxify these molecules. However, it is unclear if plants sense xenobiotics, and activate an analogous signalling system leading to their detoxification. Using the liverwort Marchantia polymorpha, we tested the hypothesis that there is a sensing system in plants that perceives herbicides resulting in the increased transcription of genes encoding proteins that detoxify these herbicides. Consistent with the hypothesis, we show that chlorsulfuron-treatment induces changes in the M. polymorpha transcriptome. However, these transcriptome changes do not occur in chlorsulfuron (CS)-treated target site resistant mutants, where the gene encoding the target carries a mutation that confers resistance to chlorsulfuron. Instead, we show that inactivation of the chlorsulfuron target, acetolactate synthase (ALS) (also known as acetohydroxyacid synthase (AHAS)), is required for the transcriptome response. These data demonstrate that the transcriptome changes in chlorsulfuron-treated plants are caused by disrupted amino acid synthesis and metabolism resulting from acetolactate synthase inhibition, and indicate that the transcriptome changes are not caused by a herbicide sensing mechanism.

Aldo-keto reductase may contribute to glyphosate resistance in Lolium rigidum

BACKGROUND

We have previously demonstrated that an aldo-keto reductase (AKR) from Echinochloa colona (EcAKR4-1) can metabolize glyphosate and confers glyphosate resistance. This study aims to investigate if the EcAKR4-1 orthologs from Lolium rigidum also play a role in glyphosate resistance in non-target-site based, glyphosate-resistant (R) L. rigidum populations from Western Australia.

RESULTS

The full-length L. rigidum AKR gene (LrAKR4C10) orthologous to EcAKR4-1, together with a distinct LrAKR1, were cloned from plants of a glyphosate-susceptible (S) (VLR1) and three glyphosate R L. rigidum populations (WALR50, WALR60 and WALR70). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) results showed that basal expression levels of the two LrAKR genes did not differ between the R and S populations, but their expression was significantly induced by glyphosate (up to 4.3-fold) or 2,4-D treatment (up to 3.4-fold) in R populations. Escherichia coli cells transformed respectively with LrAKR4C10 and LrAKR1 were more tolerant to glyphosate. Rice (Oryza sativa) seedlings overexpressing each of the two LrAKR gene survived glyphosate rates that were lethal to the green fluorescence protein (GFP) control plants. Structural modeling predicts a similar way of glyphosate binding and detoxification by LrAKR4C10 and EcAKR4-1, but an alternative way of glyphosate binding by LrAKR1. Relatively lower capacity of the two LrAKRs in conferring glyphosate resistance than the known EcAKR4-1 was discussed in relation to structural interaction.

CONCLUSION

Glyphosate-induced higher expression of the two LrAKR genes in L. rigidum populations contributes to a moderate level of glyphosate resistance likely through enhanced glyphosate metabolism. The herbicide 2,4-D can also induce the LrAKR expression, indicating the potential antagonistic effect of 2,4-D to glyphosate. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Metamifop resistance in Echinochloa glabrescens via glutathione S-transferases-involved enhanced metabolism

BACKGROUND

Echinochloa glabrescens Munro ex Hook. f. is one of the main Echinochloa spp. seriously invading Chinese rice fields and has evolved resistance to commonly used herbicides. Previously, an E. glabrescens population (LJ-02) with suspected resistance to the acetyl-CoA carboxylase (ACCase)-inhibiting herbicide metamifop was collected. This study aimed to determine its resistance status to metamifop and investigate the internal molecular mechanisms of resistance.

RESULTS

Single-dose testing confirmed that the LJ-02 population had evolved resistance to metamifop. Gene sequencing and a relative expression assay of ACCase ruled out target-site based resistance to metamifop in LJ-02. Whole-plant bioassays revealed that, compared with the susceptible population XZ-01, LJ-02 was highly resistant to metamifop and exhibited cross-resistance to fenoxaprop-P-ethyl. Pretreatment with the known glutathione S-transferase (GST) inhibitor, 4-chloro-7-nitrobenzoxadiazole (NBD-Cl), largely reversed the resistance to metamifop by approximately 81%. Liquid chromatography-tandem mass spectrometry analysis indicated that the metabolic rates of one of the major metabolites of metamifop, N-(2-fluorophenyl)-2-hydroxy-N-methylpropionamide (HPFMA), were up to 383-fold faster in LJ-02 plants than in XZ-01 plants. There were higher basal and metamifop-inducible GST activities toward 1-chloro-2,4-dinitrobenzene (CDNB) in LJ-02 than in XZ-01. Six GST genes were metamifop-induced and overexpressed in the resistant LJ-02 population.

CONCLUSION

This study reports, for the first time, the occurrence of metabolic metamifop resistance in E. glabrescens worldwide. The high-level metamifop resistance in the LJ-02 population may mainly involve specific isoforms of GSTs that endow high catalytic activity and strong substrate specificity. © 2023 Society of Chemical Industry.

Genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with herbicide resistance evolved before the origin of land plants

Cytochrome P450 (CYP) monooxygenases and glutathione S-transferases (GST) are enzymes that catalyse chemical modifications of a range of organic compounds. Herbicide resistance has been associated with higher levels of CYP and GST gene expression in some herbicide-resistant weed populations compared to sensitive populations of the same species. By comparing the protein sequences of 9 representative species of the Archaeplastida-the lineage which includes red algae, glaucophyte algae, chlorophyte algae, and streptophytes-and generating phylogenetic trees, we identified the CYP and GST proteins that existed in the common ancestor of the Archaeplastida. All CYP clans and all but one land plant GST classes present in land plants evolved before the divergence of streptophyte algae and land plants from their last common ancestor. We also demonstrate that there are more genes encoding CYP and GST proteins in land plants than in algae. The larger numbers of genes among land plants largely results from gene duplications in CYP clans 71, 72, and 85 and in the GST phi and tau classes [1,2]. Enzymes that either metabolise herbicides or confer herbicide resistance belong to CYP clans 71 and 72 and the GST phi and tau classes. Most CYP proteins that have been shown to confer herbicide resistance are members of the CYP81 family from clan 71. These results demonstrate that the clan and class diversity in extant plant CYP and GST proteins had evolved before the divergence of land plants and streptophyte algae from a last common ancestor estimated to be between 515 and 474 million years ago. Then, early in embryophyte evolution during the Palaeozoic, gene duplication in four of the twelve CYP clans, and in two of the fourteen GST classes, led to the large numbers of CYP and GST proteins found in extant land plants. It is among the genes of CYP clans 71 and 72 and GST classes phi and tau that alleles conferring herbicide resistance evolved in the last fifty years.

Integrated omic techniques and their genomic features for invasive weeds

Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.

Identification of the key metabolites and related genes network modules highly associated with the nutrients and taste components among different Pepino (Solanum muricatum) cultivars

There is considerable knowledge about plant compounds that produce flavor, scent, and aroma. Aside from the similarities, however, groups of plant-produced nutrients and taste components have little in common with each other. Network analysis holds promise for metabolic gene discovery, which is especially important in plant systems where metabolic networks are not yet fully resolved. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions in two different pepino varieties. Differential metabolomics analysis is carried out for detection of eventual interaction of compound. We adopted a multi-omics approach to profile the transcriptome and metabolome analyze differences in phenolic acids, flavonoids, organic acids, lipids, alkaloids, and sugars between LOF and SRF. The two most predominant classes of metabolites are phenolic acids and lipids in pepino. Overall results show enrichment in most DEGs was carbohydrate and biosynthesis of secondary metabolites pathway. Results of DEMs predominantly comprised N-p-coumaroyl agmatine and tryptamine, and significant differences were observed in their expression between LOF and SRF. Integrated DEMs and DEGs specific networks were constructed by combining two types of networks: transcriptional regulatory networks composed of interactions between DEMs and the regulated genes, and pepino metabolite-metabolite interaction networks. Newly discovered features, such as DEGs (USPA, UBE2 and DELLA) involved in the production of secondary metabolites are found in coregulated gene clusters. Moreover, lipid metabolites were most involved in DEMs correlations by OPLS-DA while identifying a significant number of DEGs co-regulated by SENP1, HMGCS et al. These results further that the metabolite discrepancies result from characterized the nutrients and taste components between two pepino genotype. Among the possible causes of the differences between species in pepino metabolite concentrations is co-regulated by these DEGs, continue to suggest that novel features of metabolite biosynthetic pathway remain to be uncovered. Finally, the integrated metabolome and transcriptome analyses have revealed that many important metabolic pathways are regulated at the transcriptional level. The metabolites content differences observed among varieties of the same species mainly originates from different regulated genes and enzymes expression. Overall, this study provides new insights into the underlying causes of differences in the plant metabolites and suggests that genetic data can be used to improve its nutrients and taste components.

Diverse mechanisms associated with cyhalofop-butyl resistance in Chinese sprangletop (Leptochloa chinensis (L.) Nees): Characterization of target-site mutations and metabolic resistance-related genes in two resistant populations

Resistance of Chinese sprangletop (Leptochloa chinensis (L.) Nees) to the herbicide cyhalofop-butyl has recently become a severe problem in rice cultivation. However, the molecular mechanisms of target-site resistance (TSR) in cyhalofop-butyl-resistant L. chinensis as well as the underlying non-target-site resistance (NTSR) have not yet been well-characterized. This study aimed to investigate cyhalofop-butyl resistance mechanisms using one susceptible population (LC-S) and two resistant populations (LC-1701 and LC-1704) of L. chinensis. We analyzed two gene copies encoding the entire carboxyltransferase (CT) domain of chloroplastic acetyl-CoA carboxylase (ACCase) from each population. Two non-synonymous substitutions were detected in the resistant L. chinensis populations (Trp²⁰²⁷-Cys in the ACCase1 of LC-1701 and Leu¹⁸¹⁸-Phe in the ACCase2 of LC-1704), which were absent in LC-S. As Trp²⁰²⁷-Cys confers resistance to ACCase-inhibiting herbicides, the potential relationship between the novel Leu¹⁸¹⁸-Phe mutation and cyhalofop-butyl resistance in LC-1704 was further explored by single-nucleotide polymorphism (SNP) detection. Metabolic inhibition assays indicated that cytochrome P450 monooxygenases (P450s) and glutathione S-transferases (GSTs) contributed to cyhalofop-butyl resistance in specific resistant populations. RNA sequencing showed that the P450 genes CYP71Z18, CYP71C4, CYP71C1, CYP81Q32, and CYP76B6 and the GST genes GSTF11, GSTF1, and GSTU6 were upregulated in at least one resistant population, which indicated their putative roles in cyhalofop-butyl resistance of L. chinensis. Correlation analyses revealed that the constitutive or inducible expression patterns of CYP71C4, CYP71C1, GSTF1, and GSTU6 in L. chinensis were strongly associated with the resistant phenotype. For this reason, attention should be directed towards these genes to elucidate metabolic resistance to cyhalofop-butyl in L. chinensis. The findings of this study improve the understanding of mechanisms responsible for resistance to ACCase-inhibiting herbicides in grass-weed species at the molecular level, thus aiding in the development of weed management strategies that delay the emergence of resistance to this class of pest control products.

Directed Evolution of Phi Class Glutathione Transferases Involved in Multiple-Herbicide Resistance of Grass Weeds and Crops

The extensive application of herbicides in crop cultivation has indisputably led to the emergence of weed populations characterized by multiple herbicide resistance (MHR). This phenomenon is associated with the enhanced metabolism and detoxifying ability of endogenous enzymes, such as phi class glutathione transferases (GSTFs). In the present work, a library of mutant GSTFs was created by in vitro directed evolution via DNA shuffling. Selected gstf genes from the weeds Alopecurus myosuroides and Lolium rigidum, and the cereal crops Triticum durum and Hordeum vulgare were recombined to forge a library of novel chimeric GSTFs. The library was activity screened and the best-performing enzyme variants were purified and characterized. The work allowed the identification of enzyme variants that exhibit an eight-fold improvement in their catalytic efficiency, higher thermal stability (8.3 °C) and three-times higher inhibition sensitivity towards the herbicide butachlor. The crystal structures of the best-performing enzyme variants were determined by X-ray crystallography. Structural analysis allowed the identification of specific structural elements that are responsible for k_cat regulation, thermal stability and inhibition potency. These improved novel enzymes hold the potential for utilization in biocatalysis and green biotechnology applications. The results of the present work contribute significantly to our knowledge of the structure and function of phi class plant GSTs and shed light on their involvement in the mechanisms of MHR.

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.

Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots

Herbicides are key weed-control tools, but their repeated use across large areas has favored the evolution of herbicide resistance. Although target-site has been the most prevalent and studied type of resistance, non-target-site resistance (NTSR) is increasing. However, the genetic factors involved in NTSR are widely unknown. In this study, four gene groups encoding putative NTSR enzymes, namely, cytochrome-P450, glutathione-S-transferase (GST), uridine 5'-diphospho-glucuronosyltransferase (UDPGT), and nitronate monooxygenase (NMO) were analyzed. The monocot and dicot gene sequences were downloaded from publicly available databases. Phylogenetic trees revealed that most of the CYP450 resistance-related sequences belong to CYP81 (5), and in GST, most of the resistance sequences belonged to GSTU18 (9) and GSTF6 (8) groups. In addition, the study of upstream promoter sequences of these NTSR genes revealed stress-related cis-regulatory motifs, as well as eight transcription factor binding sites (TFBS) were identified. The discovered TFBS were commonly present in both monocots and dicots, and the identified motifs are known to play key roles in countering abiotic stress. Further, we predicted the 3D structure for the resistant CYP450 and GST protein and identified the substrate recognition site through the homology approach. Our description of putative NTSR enzymes may be used to develop innovative weed control techniques to delay the evolution of NTSR.

P450s mediated enhanced herbicide metabolism involved in the thifensulfuron-methyl resistance in Ipomoea purpurea L

Ipomea purpurea (L.) Roth. reduces dry land crop yield and quality in Northeast China, especially in Liaoning Province. Frequent use of thifensulfuron-methyl in recent years has resulted in herbicide resistance in I. purpurea. We evaluated resistance levels of I. purpurea to thifensulfuron-methyl, an acetolactate synthase (ALS) inhibitor, in Liaoning Province and further investigated the resistance mechanisms. The results showed that 15 populations of I. purpurea have evolved up to 5.81-34.44-fold resistance to thifensulfuron-methyl, compared to the susceptible population (S), among which LN3 was the most resistant. DNA sequencing of the ALS gene in susceptible and resistant populations did not reveal any target site mutations that could be associated with resistance to thifensulfuron-methyl in I. purpurea. Additionally, no significant difference was detected between the in vitro ALS activity of LN3 and S. The GR₅₀ of LN3 decreased sharply by 47% when malathion (a P450 inhibitor) was applied with thifensulfuron-methyl. Absorption of thifensulfuron-methyl by LN3 was equal to that of S; however, LN3 metabolized the herbicide significantly faster. This was repressed after the inhibition of P450s activity. Collectively, our results confirmed that I. purpurea in Liaoning Province has developed resistance to thifensulfuron-methyl and implied that the resistance was conferred by the increase in detoxification mediated by P450s. Furthermore, LN3 was sensitive to fluroxypyr, which can be used as an alternative to control I. purpurea.

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.

Cytochrome P450 CYP709C56 metabolizing mesosulfuron-methyl confers herbicide resistance in Alopecurus aequalis

Multiple herbicide resistance in diverse weed species endowed by enhanced herbicide detoxification or degradation is rapidly growing into a great threat to herbicide sustainability and global food safety. Although metabolic resistance is frequently documented in the economically damaging arable weed species shortawn foxtail (Alopecurus aequalis Sobol.), relevant molecular knowledge has been lacking. Previously, we identified a field population of A. aequalis (R) that had evolved metabolic resistance to the commonly used acetolactate synthase (ALS)-inhibiting herbicide mesosulfuron-methyl. RNA sequencing was used to discover potential herbicide metabolism-related genes, and four cytochrome P450s (CYP709C56, CYP71R18, CYP94C117, and CYP94E14) were identified with higher expressions in the R vs. susceptible (S) plants. Here the full-length P450 complementary DNA transcripts were each cloned with identical sequences between the S and R plants. Transgenic Arabidopsis overexpressing CYP709C56 became resistant to the sulfonylurea herbicide mesosulfuron-methyl and the triazolo-pyrimidine herbicide pyroxsulam. This resistance profile generally but does not completely in accordance with what is evident in the R A. aequalis. Transgenic lines exhibited enhanced capacity for detoxifying mesosulfuron-methyl into O-demethylated metabolite, which is in line with the detection of O-demethylated herbicide metabolite in vitro in transformed yeast. Structural modeling predicted that mesosulfuron-methyl binds to CYP709C56 involving amino acid residues Thr-328, Thr-500, Asn-129, Gln-392, Phe-238, and Phe-242 for achieving O-demethylation. Constitutive expression of CYP709C56 was highly correlated with the metabolic mesosulfuron-methyl resistance in A. aequalis. These results indicate that CYP709C56 degrades mesosulfuron-methyl and its up-regulated expression in A. aequalis confers resistance to mesosulfuron-methyl.

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.

The analysis of reference genes expression stability in susceptible and resistant Apera spica-venti populations under herbicide treatment

Weed resistance to herbicides constitutes a serious problem to world crop production. One of the weeds that are significantly threatening the crops’ yield and quality is Apera spica-venti. The target-site resistance (TSR) mechanism of A. spica-venti has been widely studied, though, little is known about its non-target-site resistance (NTSR) mechanisms at the molecular level. Molecular examination of NTSR is, to a great extent, based on the expression profiles of selected genes, e.g. those participating in detoxification. However, to obtain reliable results of gene expression analysis, the use of a normalizer is required. The aim of this study was to select the best reference genes in A. spica-venti plants of both populations, susceptible and resistant to ALS inhibitor, under treatment with herbicide. Eleven housekeeping genes were chosen for their expression stability assessment. The efficiency correction of raw quantification cycles (Cq) was included in the gene expression stability analyses, which resulted in indicating the TATA-box binding protein (TBP), glyceraldehyde-3-phosphate dehydrogenase, cytosolic (GAPC), and peptidyl-prolyl cis–trans isomerase CYP28 (CYP28) genes as the most stably expressed reference genes. The obtained results are of vital importance for future studies on the expression of genes associated with the non-target-site resistance mechanisms in the A. spica-venti populations susceptible and resistant to herbicides.

Peculiarities of nitronate monooxygenases and perspectives for in vivo and in vitro applications

Nitroalkanes such as nitromethane, nitroethane, 1-nitropropane (1NP), and 2-nitropropane (2NP), derived from anthropogenic activities, are hazardous environmental pollutants due to their toxicity and carcinogenic activity. In nature, 3-nitropropionate (3NPA) and its derivatives are produced as a defense mechanism by many groups of organisms, including bacteria, fungi, insects, and plants. 3NPA is highly toxic as its conjugate base, propionate-3-nitronate (P3N), is a potent inhibitor of mitochondrial succinate dehydrogenase, essential to the tricarboxylic acid cycle, and can inhibit isocitrate lyase, a critical enzyme of the glyoxylate cycle. In response to these toxic compounds, several organisms on the phylogenetic scale express genes that code for enzymes involved in the catabolism of nitroalkanes: nitroalkane oxidases (NAOs) and nitronate monooxygenases (NMOs) (previously classified as nitropropane dioxygenases, NPDs). Two types of NMOs have been identified: class I and class II, which differ in structure, catalytic efficiency, and preferred substrates. This review focuses on the biochemical properties, structure, classification, and physiological functions of NMOs, and offers perspectives for their in vivo and in vitro applications. KEY POINTS: • Nitronate monooxygenases (NMOs) are key enzymes in nitroalkane catabolism. • NMO enzymes are involved in defense mechanisms in different organisms. • NMO applications include organic synthesis, biocatalysts, and bioremediation.

Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed (Conyza canadensis)

The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (Conyza canadensis), compared to a susceptible biotype (TNS). A read size of 100.2 M was sequenced on the Illumina platform and subjected to de novo assembly, resulting in 77,072 gene-level contigs, of which 32,493 were uniquely annotated by a BlastX alignment of protein sequence similarity. The most differentially expressed genes were enriched in the gene ontology (GO) term of the transmembrane transport protein. In addition, fifteen upregulated genes were identified in TNR after glyphosate treatment but were not detected in TNS. Ten of these upregulated genes were transmembrane transporter or kinase receptor proteins. Therefore, a combination of changes in gene expression among transmembrane receptor and kinase receptor proteins may be important for endowing non-target-site glyphosate-resistant C. canadensis.

Antibiotic resistance lessons for the herbicide resistance crisis

The challenges of resistance to antibiotics and resistance to herbicides have much in common. Antibiotic resistance became a risk in the 1950s, but a concerted global effort to manage it did not begin until after 2000. Widespread herbicide use began during the 1950s and was soon followed by an unabated rise in resistance. Here, we examine what lessons for combatting herbicide resistance could be learnt from the global, coordinated efforts of all stakeholders to avert the antibiotic resistance crisis. © 2021 Society of Chemical Industry.

Understanding Resistance Mechanisms to Trifluralin in an Arkansas Palmer Amaranth Population

Amaranthus palmeri S. Watson (Palmer amaranth) is considered a problematic and troublesome weed species in many crops in the USA, partly because of its ability to evolve resistance to herbicides. In this study, we explored the mechanism of resistance in a trifluralin-resistant A. palmeri accession collected from Arkansas, USA. Dose-response assays using agar plates demonstrated an EC₅₀ (effective concentration that reduces root length by 50%) of 1.02 µM trifluralin compared to 0.39 µM obtained in the susceptible accession. Thus, under these conditions, the resistant accession required 2.6 times more trifluralin to inhibit root length by 50%. Seeds in the presence or absence of the cytochrome P450-inhibitior malathion displayed a differential response with no significant influence on root length, suggesting that resistance is not P450-mediated. In addition, application of 4-chloro-7-nitrobenzofurazan (NBD-Cl), a glutathione S-transferase (GST) inhibitor, showed significant differences in root length, indicating that GSTs are most likely involved in the resistance mechanism. Sequencing of α- and β-tubulin genes revealed no single nucleotide polymorphisms (SNPs) previously described between accessions. In addition, relative gene copy number of α- and β-tubulin genes were estimated; however, both resistant and susceptible accessions displayed similar gene copy numbers. Overall, our results revealed that GST-mediated metabolism contributes to trifluralin resistance in this A. palmeri accession from Arkansas.

Expression stability of internal reference gene in response to Trichoderma polysporum infection in Avena fatua L

Trichoderma polysporum was a pathogenic fungi which showed strong pathogenicity to Avena fatua L. in recent study. The stress response of A. fatua to T. polysporum is mediated by the regulation of gene expression. Quantification of the expression of genes requires normalizing RT-qPCR data using reference genes with stable expression in the system studied as internal standards. To construct a RT-qPCR system suitable for response of A. fatua to T. polysporum, and screen stable internal reference genes, GeNorm, NormFinder, BestKeeper and RefFinde were used to perform SYBR Green-based RT-qPCR analysis on eight candidate internal reference genes (18S, 28S, TUA, UBC, ACT, GAPDH, TBP and EF-1α) in A. fatua samples after inoculation of T. polysporum Strain HZ-31. The results showed that TBP, 18S and UBC were the most stable internal reference genes, TBP and TUA, TBP and GAPDH, 18S and TBP, UBC and 18S were the most suitable combination of the two internal reference genes, which could be used as internal reference genes for functional gene expression analysis during the interaction between T. polysporum and A. fatua. This is the first study describing a set of reference genes with a stable expression under fungi stress in A. fatua. These genes are also candidate reference genes of choice for studies seeking to identify stress-responsive genes in A. fatua.

Identification of the most suitable reference gene for gene expression studies with development and abiotic stress response in Bromus sterilis

Bromus sterilis is an annual weedy grass, causing high yield losses in winter cereals. Frequent use of herbicides had led to the evolution of herbicide resistance in this species. Mechanisms underlying herbicide resistance in B. sterilis must be uncovered because this problem is becoming a global threat. qRT-PCR and the next-generation sequencing technologies can elucidate the resistance mechanisms. Although qRT-PCR can calculate precise fold changes, its preciseness depends on the expression of reference genes. Regardless of stable expression in any given condition, no gene can act as a universal reference gene. Hence, it is necessary to identify the suitable reference gene for each species. To our knowledge, there are no reports on the suitable reference gene in any brome species so far. Thus, in this paper, the stability of eight genes was evaluated using qRT-PCR experiments followed by expression stability ranking via five most commonly used software for reference gene selection. Our findings suggest using a combination of 18S rRNA and ACCase to normalise the qRT-PCR data in B. sterilis. Besides, reference genes are also recommended for different experimental conditions. The present study outcomes will facilitate future molecular work in B. sterilis and other related grass species.

Enhanced metabolism confers a high level of cyhalofop-butyl resistance in a Chinese sprangletop (Leptochloa chinensis (L.) Nees) population

BACKGROUND

Chinese sprangletop (Leptochloa chinensis (L.) Nees) is one of main grass weeds invading Chinese rice fields. The target-site resistance (TSR) of cyhalofop-butyl have been widely reported in L. chinensis populations, but the non-target-site resistance (NTSR) mechanisms have not yet been well-characterized. This study aims to investigate the likely NTSR in a cyhalofop-butyl-resistant L. chinensis population (YZ-R), which was collected from Yangzhou city, Jiangsu Province, China.

RESULTS

Dose-response assays showed the YZ-R population exhibited 191.6-fold resistance to cyhalofop-butyl, compared to the susceptible population (YZ-S). This resistance is not target-site based, because no mutations in the two ACCase genes were detected in the YZ-R plants compared to the YZ-S plants, and the ACCase genes expression levels were similar in YZ-S and YZ-R plants. In addition, the cytochrome P450 inhibitor malathion and piperonyl butoxide (PBO), and glutathione S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) did not significantly reverse cyhalofop-butyl resistance in the YZ-R population. However, liquid chromatography-mass spectrometry (LC-MS) analysis indicated that the metabolic rates of cyhalofop acid in YZ-R plants was significantly faster (5 to 10- fold) than in YZ-S plants. Furthermore, the YZ-R population showed no cross-resistance to other ACCase-inhibiting herbicides.

CONCLUSION

These results indicated that cyhalofop-butyl resistance in the YZ-R population is due to non-target-site based enhanced herbicide metabolism. Resistance in this population is likely involved in a specific detoxification enzyme, with possible high catalytic efficiency and strong substrate specificity, therefore leading to high-level and single resistance to cyhalofop-butyl. © 2021 Society of Chemical Industry.

Enhanced metabolism and target gene overexpression confer resistance against acetolactate synthase-inhibiting herbicides in Bromus sterilis

BACKGROUND

Intensive application of acetolactate synthase (ALS)-inhibiting herbicides has resulted in herbicide-resistance in many weeds, including Bromus sterilis. The present study was conducted to identify the mechanisms conferring resistance to ALS-inhibiting herbicides in a Bromus sterilis biotype.

RESULTS

Dose-response studies revealed the resistant biotype to be 288 times less sensitive to pyroxsulam than the susceptible biotype. Furthermore, experiment with a single-dose, proved this biotype was also cross-resistant to propoxycarbazone, iodosulfuron plus mesosulfuron and sulfosulfuron. Prior treatment with malathion, a known inhibitor of cytochrome P450s, reduced the level of resistance to pyroxsulam. No mutations were detected from the partial ALS gene sequencing. Flow cytometry and chromosome counting rejected ploidy level variation between the susceptible and resistant biotypes. Relative copy number variation ruled out gene amplification. Quantitative real-time polymerase chain reaction (PCR) detected a significant difference in ALS gene expression between the susceptible and resistant biotypes.

CONCLUSIONS

Target gene overexpression and enhanced metabolism by cytochrome P450s are likely mechanisms of resistance to pyroxsulam in Bromus sterilis. The current findings highlight the need to monitor additional brome populations for herbicide resistance in Europe and endorse the need for alternate herbicides in integrated weed management to delay the possible evolution of herbicide resistance in these species. © 2020 Society of Chemical Industry.

Insights into the Role of Transcriptional Gene Silencing in Response to Herbicide-Treatments in Arabidopsis thaliana

Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether transcriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly increased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregulated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment.

Non-target Site Herbicide Resistance Is Conferred by Two Distinct Mechanisms in Black-Grass (Alopecurus myosuroides)

Non-target site resistance (NTSR) to herbicides in black-grass (Alopecurus myosuroides) results in enhanced tolerance to multiple chemistries and is widespread in Northern Europe. To help define the underpinning mechanisms of resistance, global transcriptome and biochemical analysis have been used to phenotype three NTSR black-grass populations. These comprised NTSR1 black-grass from the classic Peldon field population, which shows broad-ranging resistance to post-emergence herbicides; NTSR2 derived from herbicide-sensitive (HS) plants repeatedly selected for tolerance to pendimethalin; and NTSR3 selected from HS plants for resistance to fenoxaprop-P-ethyl. NTSR in weeds is commonly associated with enhanced herbicide metabolism catalyzed by glutathione transferases (GSTs) and cytochromes P450 (CYPs). As such, the NTSR populations were assessed for their ability to detoxify chlorotoluron, which is detoxified by CYPs and fenoxaprop-P-ethyl, which is acted on by GSTs. As compared with HS plants, enhanced metabolism toward both herbicides was determined in the NTSR1 and NTSR2 populations. In contrast, the NTSR3 plants showed no increased detoxification capacity, demonstrating that resistance in this population was not due to enhanced metabolism. All resistant populations showed increased levels of AmGSTF1, a protein functionally linked to NTSR and enhanced herbicide metabolism. Enhanced AmGSTF1 was associated with increased levels of the associated transcripts in the NTSR1 and NTSR2 plants, but not in NTSR3, suggestive of both pre- and post-transcriptional regulation. The related HS, NTSR2, and NTSR3 plants were subject to global transcriptome sequencing and weighted gene co-expression network analysis to identify modules of genes with coupled regulatory functions. In the NTSR2 plants, modules linked to detoxification were identified, with many similarities to the transcriptome of NTSR1 black-grass. Critical detoxification genes included members of the CYP81A family and tau and phi class GSTs. The NTSR2 transcriptome also showed network similarities to other (a)biotic stresses of plants and multidrug resistance in humans. In contrast, completely different gene networks were activated in the NTSR3 plants, showing similarity to the responses to cold, osmotic shock and fungal infection determined in cereals. Our results demonstrate that NTSR in black-grass can arise from at least two distinct mechanisms, each involving complex changes in gene regulatory networks.

Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides

BACKGROUND

Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping-by-sequencing and population-level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome-wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance.

RESULTS

Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site-associated DNA (RAD)-sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (F_ST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (F_IS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population-level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers.

CONCLUSION

There is likely extensive human-mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry.

Innate promiscuity of the CYP706 family of P450 enzymes provides a suitable context for the evolution of dinitroaniline resistance in weed

Increased metabolism is one of the main causes for evolution of herbicide resistance in weeds, a major challenge for sustainable food production. The molecular drivers of this evolution are poorly understood. We tested here the hypothesis that a suitable context for the emergence of herbicide resistance could be provided by plant enzymes with high innate promiscuity with regard to their natural substrates. A selection of yeast-expressed plant cytochrome P450 enzymes with well documented narrow to broad promiscuity when metabolizing natural substrates was tested for herbicide metabolism competence. The positive candidate was assayed for capacity to confer herbicide tolerance in Arabidopsis thaliana. Our data demonstrate that Arabidopsis thaliana CYP706A3, with the most promiscuous activity on monoterpenes and sesquiterpenes for flower defence, can also oxidize plant microtubule assembly inhibitors, dinitroanilines. Ectopic overexpression of CYP706A3 confers dinitroaniline resistance. We show, in addition, that the capacity to metabolize dinitroanilines is shared by other members of the CYP706 family from plants as diverse as eucalyptus and cedar. Supported by three-dimensional (3D) modelling of CYP706A3, the properties of enzyme active site and substrate access channel are discussed together with the shared physicochemical properties of the natural and exogenous substrates to explain herbicide metabolism.

Multiple Herbicide Resistance Evolution: The Case of Eleusine indica in Brazil

The occurrence of multiple herbicide resistant weeds has increased considerably in glyphosate-resistant soybean fields in Brazil; however, the mechanisms governing this resistance have not been studied. In its study, the target-site and nontarget-site mechanisms were characterized in an Eleusine indica population (R-15) with multiple resistance to the acetyl-CoA carboxylase (ACCase) inhibitors, glyphosate, imazamox, and paraquat. Absorption and translocation rates of 14C-diclofop-methyl14C-imazamox and 14C-glyphosate of the R-15 population were similar to those of a susceptible (S-15) population; however, the R-15 population translocated ∼38% less 14C-paraquat to the rest of plant and roots than the S-15 population. Furthermore, the R-15 plants metabolized (by P450 cytochrome) 55% and 88% more diclofop-methyl (conjugate) and imazamox (imazamox-OH and conjugate), respectively, than the S-15 plants. In addition, the Pro-106-Ser mutation was found in the EPSPS gene of this population. This report describes the first characterization of the resistance mechanisms in a multiple herbicide resistant weed from Brazil.

Diversity of α-tubulin transcripts in Lolium rigidum

BACKGROUND

Tubulin, the target site of dinitroaniline herbicides, is encoded by small gene families in plants. To better characterize the mechanisms of target-site resistance to dinitroaniline herbicides in the globally important weedy species Lolium rigidum, attempts were made to amplify and sequence α-tubulin transcripts.

RESULTS

Four α-tubulin isoforms (TUA1, TUA2, TUA3 and TUA4) were identified in L. rigidum. Variations in the number and sequence of transcripts encoding these α-tubulin proteins were found in individuals from the two L. rigidum populations examined. Within and among populations, differences in the 5'- and 3'-untranslated regions of cDNA in TUA3 and TUA4 were identified. Furthermore, a novel double mutation, Arg-390-Cys+Asp-442-Glu, in the TUA3 transcript was identified and has the potential to confer dinitroaniline resistance.

CONCLUSION

This research reveals the complexity of the α-tubulin gene family in individuals/populations of the cross-pollinated weedy species L. rigidum, and highlights the need for better understanding of the molecular architecture of tubulin gene families for detecting resistance point mutations. Although TUA4 is a commonly expressed α-tubulin isoform containing most frequently reported resistance mutations, other mutant tubulin isoforms may also have a role in conferring dinitroaniline resistance.

Non-target-Site Resistance in Lolium spp. Globally: A Review

The Lolium genus encompasses many species that colonize a variety of disturbed and non-disturbed environments. Lolium perenne L. spp. perenne, L. perenne L. spp. multiflorum, and L. rigidum are of particular interest to weed scientists because of their ability to thrive in agricultural and non-agricultural areas. Herbicides are the main tool to control these weeds; however, Lolium spp. populations have evolved multiple- and cross-resistance to at least 14 herbicide mechanisms of action in more than 21 countries, with reports of multiple herbicide resistance to at least seven mechanisms of action in a single population. In this review, we summarize what is currently known about non-target-site resistance in Lolium spp. to acetyl CoA carboxylase, acetohydroxyacid synthase, microtubule assembly, photosystem II, 5-enolpyruvylshikimate-3-phosphate synthase, glutamine synthetase, very-long chain fatty acids, and photosystem I inhibitors. We suggest research topics that need to be addressed, as well as strategies to further our knowledge and uncover the mechanisms of non-target-site resistance in Lolium spp.

Cytochrome P450 CYP81A10v7 in Lolium rigidum confers metabolic resistance to herbicides across at least five modes of action

Rapid and widespread evolution of multiple herbicide resistance in global weed species endowed by increased capacity to metabolize (degrade) herbicides (metabolic resistance) is a great threat to herbicide sustainability and global food production. Metabolic resistance in the economically damaging crop weed species Lolium rigidum is well known but a molecular understanding has been lacking. We purified a metabolic resistant (R) subset from a field evolved R L. rigidum population. The R, the herbicide susceptible (S) and derived F₂ populations were used for candidate herbicide resistance gene discovery by RNA sequencing. A P450 gene CYP81A10v7 was identified with higher expression in R vs. S plants. Transgenic rice overexpressing this Lolium CYP81A10v7 gene became highly resistant to acetyl-coenzyme A carboxylase- and acetolactate synthase-inhibiting herbicides (diclofop-methyl, tralkoxydim, chlorsulfuron) and moderately resistant to hydroxyphenylpyruvate dioxygenase-inhibiting herbicide (mesotrione), photosystem II-inhibiting herbicides (atrazine and chlorotoluron) and the tubulin-inhibiting herbicide trifluralin. This wide cross-resistance profile to many dissimilar herbicides in CYP81A10v7 transgenic rice generally reflects what is evident in the R L. rigidum. This report clearly showed that a single P450 gene in a cross-pollinated weed species L. rigidum confers resistance to herbicides of at least five modes of action across seven herbicide chemistries.

RNA-Seq transcriptome analysis to identify candidate genes involved in non-target site-based mesosulfuron-methyl resistance in Beckmannia syzigachne

American sloughgrass (Beckmannia syzigachne Steud.) has become a dominant weed in fields with rice-wheat rotation. Moreover, herbicide resistance has rendered weed control difficult. We identified a biotype showing resistance to ALS inhibitor mesosulfuron-methyl with a resistant index 3.3, but without any ALS mutation. This study aims to identify and confirm the factors associated with non-target site resistance of this biotype to mesosulfuron-methyl using RNA-Seq. 118,111 unigenes were assembled, and 50.9% of these were annotated across seven databases. Eleven contigs related to metabolic resistance were identified based on differential expression via RNA-Seq which include a novel resistance-related transcription factor (MYC3) and two disease resistance proteins were also identified (At1g58602 and At1g15890). Fold changes in expression of these genes in comparison M-R vs. M-S ranged from 3.9 to 11.6, as confirmed by qPCR. The expression of a contig annotated as cytochrome P450 (CYP86B1) in resistant individuals was over 3 times higher than that in sensitive individuals at 0-72 h after mesosulfuron-methyl treatment. A similar trend was noted for three other genes annotated as glutathione S-transferase (GST), namely GST-T3, GST-U6, and GST-U14; the expression of GST-U6 in resistant individuals was up to 142.3 times higher than that in sensitive individuals at 24 h after mesosulfuron-methyl treatment. In addition, GST activity in resistant individuals was 2.1 to 5.3 times higher than that in sensitive individuals. The GR₅₀ of resistant biotype decreased from 24.4 to 11.3 g a.i. ha^-1 after P450 inhibitor malathion treatment. This study identified a cytochrome P450 gene CYP86B1 and three GST genes GST-T3, GST-U6, and GST-U14 that have higher expression in mesosulfuron-methyl resistant B. syzigachne, suggesting that both P450- and GST-based activities could be involved in resistance.

Diversified Resistance Mechanisms in Multi-Resistant Lolium spp. in Three European Countries

Annual ryegrass species (Lolium spp.) infest cereal crops worldwide. Ryegrass populations with multiple resistance to the acetyl coenzyme A carboxylase (ACCase) and acetolactate synthase (ALS) inhibitors are an increasing problem in several European countries. We investigated the resistance pattern and level of resistance in ryegrass populations collected in Denmark, Greece and Italy and studied the diversity of mechanisms endowing resistance, both target-site and metabolism based. All populations showed high resistance indexes (RI) to the ALS inhibitors, iodosufuron-methyl-sodium + mesosulfuron-methyl (RI from 8 to 70), whereas the responses to the two ACCase inhibitors, clodinafop-propargyl and pinoxaden, differed. The Greek and Italian populations were moderately to highly resistant to clodinafop (RI > 8) and showed low to moderate resistance to pinoxaden (RI ranged from 3 to 13) except for one Italian population. In contrast, the Danish Lolium populations showed low to moderate resistance to clodinafop (RI ranged from 2 to 7) and only one population was resistant to pinoxaden. Different mutant ACCase alleles (Leu₁₇₈₁, Cys₂₀₂₇, Asn₂₀₄₁, Val₂₀₄₁, Gly₂₀₇₈, Arg₂₀₈₈, Ala₂₀₉₆) and ALS alleles (Gly₁₂₂, Ala₁₉₇, Gln₁₉₇, Leu₁₉₇, Ser₁₉₇, Thr₁₉₇, Val₂₀₅, Asn₃₇₆, Glu₃₇₆, Leu₅₇₄) endowing resistance were detected in the Greek and Italian populations. In several plants, no mutated ALS and ACCase alleles were found showing a great heterogeneity within and among the Greek and Italian populations. Conversely, no mutant ACCase alleles were identified in the four Danish populations and only one mutant ALS allele (Leu₅₇₄) was detected in two Danish populations. The expression level of nitronate monooxygenase (NMO), glutathione S-transferase (GST) and cytochrome P450s (CYP72A1 and CYP72A2) varied broadly among populations and individual plants within the populations. Constitutive up-regulation of GST, CYP72A1 and CYP72A2 was detected in resistant plants respect to susceptible plants in one Danish and one Italian population. It appears that the mechanisms underlying resistance are rather complex and diversified among Lolium spp. populations from the three countries, coevolution of both target-site resistance and metabolic based herbicide resistance appears to be a common feature in Denmark and Italy. This must be considered and carefully evaluated in adopting resistance management strategies to control Lolium spp. in cereal crops.

GJ, Guo H, Yu Q, Powles SB. Mechanistic basis for synergism of 2,4-D amine and metribuzin in Avena sterilis

The combination of herbicides with different modes of action has been adopted not only to improve weed control but also to increase the environmental sustainability of plant-protection products. In this study, we showed a synergistic effect of the auxin herbicide 2,4-D amine with the PSII-inhibiting herbicide metribuzin to control the global grass weed wild oat (Avena sterilis) population and investigated the underlying mechanisms. Pretreatment with 2,4-D amine did not change the foliar absorption of metribuzin but did increase metribuzin translocation to the roots and new leaves, although enhancement of the metribuzin metabolism was also observed. Considering that the expression level of the target site psbA gene is significantly higher in leaves than in roots, increased metribuzin translocation to new leaves is likely the major cause of the observed synergism, even though enhanced metribuzin metabolism may offset the metribuzin efficacy. This is the first report on the synergistic mechanism between 2,4-D amine and metribuzin in weed control.

Quizalofop-p-ethyl resistance in Polypogon fugax involves glutathione S-transferases

BACKGROUND

Asia minor bluegrass (Polypogon fugax) is one of the main weeds invading Chinese canola fields. The P. fugax resistant population SC-R, which survived quizalofop-p-ethyl at the field-recommended rate (67.5 g ha^-1 ), was collected from a canola field in Qingsheng County in China. The present study aimed to (1) characterize the SC-R resistance pattern to acetyl-CoA carboxylase (ACCase)-inhibiting herbicides, and (2) investigate the mechanism of quizalofop-p-ethyl resistance in this population.

RESULTS

Dose-response studies showed that resistance to quizalofop-p-ethyl and haloxyfop occurred in the SC-R population. Four transcripts/genes encoding the plastidic ACCase carboxyl-transferase domain were isolated from the P. fugax plants. No mutations in the four ACCase genes were detected in the SC-R population compared to the SC-S population. Pre-treatment with the known glutathione S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole (NBDCl), reversed resistance to quizalofop-p-ethyl and partially reversed resistance to haloxyfop-R-methyl in the resistant population (SC-R). However, the cytochrome P450 inhibitor malathion did not reverse the resistance. There was no difference in basal GST activity (using CDNB as a substrate), but there was higher inducible GST activity in SC-R relative to SC-S. Two GST genes, GST2c and GSTL3, were constitutively overexpressed in the resistant SC-R population.

CONCLUSION

This study confirmed that resistance to quizalofop-p-ethyl in the resistant P. fugax population is likely nontarget-site based involving GST, and this resistance mechanism also partially confers haloxyfop-R-methyl resistance. © 2020 Society of Chemical Industry.

Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance

In the last decade, Amaranthus tuberculatus has evolved resistance to 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-hydroxyphenylpyruvate dioxygenase inhibitors in multiple states across the midwestern United States. Two populations resistant to both mode-of-action groups, one from Nebraska (NEB) and one from Illinois (CHR), were studied using an RNA-seq approach on F2 mapping populations to identify the genes responsible for resistance. Using both an A. tuberculatus transcriptome assembly and a high-quality grain amaranth (A. hypochondriacus) genome as references, differential transcript and gene expression analyses were conducted to identify genes that were significantly over- or underexpressed in resistant plants. When these differentially expressed genes (DEGs) were mapped on the A. hypochondriacus genome, physical clustering of the DEGs was apparent along several of the 16 A. hypochondriacus scaffolds. Furthermore, single-nucleotide polymorphism calling to look for resistant-specific (R) variants, and subsequent mapping of these variants, also found similar patterns of clustering. Specifically, regions biased toward R alleles overlapped with the DEG clusters. Within one of these clusters, allele-specific expression of cytochrome  P450  81E8 was observed for 2,4-D resistance in both the CHR and NEB populations, and phylogenetic analysis indicated a common evolutionary origin of this R allele in the two populations.

Identification and expression of main genes involved in non-target site resistance mechanisms to fenoxaprop-p-ethyl in Beckmannia syzigachne

BACKGROUND

Non-target-site resistance (NTSR) to herbicides is a serious threat to global agriculture. Although metabolic resistance is the dominant mechanism of NTSR, the molecular mechanisms are not yet well-characterized. This study aimed to uncover the likely metabolism-related genes in Beckmannia syzigachne (American sloughgrass) resistant to fenoxaprop-p-ethyl.

RESULTS

Ultra-performance liquid chromatography - tandem mass spectrometry experiments showed that the resistant American sloughgrass biotype (R, SD-04-SS) showed enhanced degradation of this herbicide compared to the susceptible biotype (S, SD-12). R and S biotype were harvested at 24 h after fenoxaprop-p-ethyl treatment to conduct RNA sequencing (RNA-Seq) analysis to investigate the likely fenoxaprop-p-ethyl metabolic genes. The RNA-Seq libraries yield 417 969 980 clean reads. The de novo assembly generated 115 112 unigenes, of which 57 906 unigenes were annotated. Finally, we identified 273 cytochrome P450s, 178 oxidases, 47 glutathione S-transferases (GSTs), 166 glucosyltransferases (GTs) and 180 ABC transporter genes to determine the likely fenoxaprop-p-ethyl metabolism-related genes in R biotype. Twelve overlapping up-regulated genes in the R biotype (fenoxaprop-p-ethyl-treated R/non-treated R, fenoxaprop-p-ethyl-treated R/fenoxaprop-p-ethyl-treated S) were identified by RNA-Seq and the results were validated using qRT-PCR. Ten were identified as fenoxaprop-p-ethyl metabolism-related genes, including three P450s (homologous to CYP71D7, CYP99A2 and CYP71D10), one GST (homologous to GSTF1), two GTs (homologous to UGT90A1 and UGT83A1) and four oxidase genes.

CONCLUSION

This work demonstrates that the NTSR mechanism by means of enhanced detoxification of fenoxaprop-p-ethyl in American sloughgrass is very likely driven by herbicide metabolism related genes. The RNA-Seq data presented here provide a valuable resource for understanding the molecular mechanism of NTSR in American sloughgrass. © 2020 Society of Chemical Industry.