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Optimizing RNA‐seq studies to investigate herbicide resistance
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/ps.3318openalex-snapshot
Unravelling the genetic bases of non‐target‐site‐based resistance (NTSR) to herbicides: a major challenge for weed science in the forthcoming decade
inferredcites →https://doi.org/10.1002/ps.4605openalex-snapshot
Intensive herbicide use has selected for constitutively elevated levels of stress‐responsive mRNAs and proteins in multiple herbicide‐resistant Avena fatua L
inferredcites →https://doi.org/10.1007/s00122-005-1947-2openalex-snapshot
Recurrent selection with reduced herbicide rates results in the rapid evolution of herbicide resistance in Lolium rigidum
inferredcites →https://doi.org/10.1007/s001220000528openalex-snapshot
Effects of genetic background and environment on QTLs and epistasis for rice (Oryza sativa L.) panicle number
inferredcites →https://doi.org/10.1007/s11103-015-0292-3openalex-snapshot
RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance
inferredcites →https://doi.org/10.1007/s12041-015-0493-1openalex-snapshot
De novo characterization of the alligator weed (Alternanthera philoxeroides) transcriptome illuminates gene expression under potassium deprivation
inferredcites →https://doi.org/10.1016/j.febslet.2009.10.036openalex-snapshot
Correlation of mRNA and protein in complex biological samples
inferredcites →https://doi.org/10.1016/j.plantsci.2017.01.009openalex-snapshot
Transcriptional markers enable identification of rye-grass ( Lolium sp.) plants with non-target-site-based resistance to herbicides inhibiting acetolactate-synthase
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/nmeth.4324openalex-snapshot
Differential analysis of RNA-seq incorporating quantification uncertainty
inferredcites →https://doi.org/10.1086/285938openalex-snapshot
Surveying Patterns in the Cost of Resistance in Plants
inferredcites →https://doi.org/10.1093/bioinformatics/btt015openalex-snapshot
Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression
inferredcites →https://doi.org/10.1093/jxb/erv565openalex-snapshot
Establishing a herbicide-metabolizing enzyme library inBeckmannia syzigachneto identify genes associated with metabolic resistance
inferredcites →https://doi.org/10.1104/pp.109.3.945openalex-snapshot
Comparison of Metallothionein Gene Expression and Nonprotein Thiols in Ten Arabidopsis Ecotypes (Correlation with Copper Tolerance)
inferredcites →https://doi.org/10.1111/j.1461-0248.2004.00684.xopenalex-snapshot
Conceptual issues in local adaptation
inferredcites →https://doi.org/10.1111/tpj.12514openalex-snapshot
RNA ‐Seq transcriptome analysis to identify genes involved in metabolism‐based diclofop resistance in Lolium rigidum
inferredcites →https://doi.org/10.1111/tpj.13395openalex-snapshot
Investigating the mechanisms of glyphosate resistance in goosegrass (Eleusine indica (L.) Gaertn.) by RNA sequencing technology
inferredcites →https://doi.org/10.1146/annurev-arplant-042809-112119openalex-snapshot
Evolution in Action: Plants Resistant to Herbicides
inferredcites →https://doi.org/10.1186/1471-2164-14-18openalex-snapshot
Genetic variation and expression diversity between grain and sweet sorghum lines
inferredcites →https://doi.org/10.1186/s12864-015-1627-9openalex-snapshot
Glyphosate’s impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching
inferredcites →https://doi.org/10.1186/s12864-015-1767-yopenalex-snapshot
Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq
inferredcites →https://doi.org/10.1186/s12864-015-1804-xopenalex-snapshot
ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass)
inferredcites →https://doi.org/10.1186/s12864-016-2915-8openalex-snapshot
Target-site and non-target-site based resistance to the herbicide tribenuron-methyl in flixweed (Descurainia sophia L.)
inferredcites →https://doi.org/10.1186/s12870-015-0528-zopenalex-snapshot
RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum
inferredcites →https://doi.org/10.1261/rna.046011.114openalex-snapshot
Power analysis and sample size estimation for RNA-Seq differential expression
inferredcites →https://doi.org/10.1371/journal.pone.0069168openalex-snapshot
De novo Assembly and Characterization of the Barnyardgrass (Echinochloa crus-galli) Transcriptome Using Next-Generation Pyrosequencing
inferredcites →https://doi.org/10.1371/journal.pone.0099940openalex-snapshot
Transcriptome Profiling to Discover Putative Genes Associated with Paraquat Resistance in Goosegrass (Eleusine indica L.)
inferredcites →https://doi.org/10.1534/g3.114.013508openalex-snapshot
De Novo Assembly and Annotation of the Transcriptome of the Agricultural Weed Ipomoea purpurea Uncovers Gene Expression Changes Associated with Herbicide Resistance
inferredcites →https://doi.org/10.3389/fpls.2017.01391openalex-snapshot
Transcriptome Profiling to Identify Genes Involved in Mesosulfuron-Methyl Resistance in Alopecurus aequalis
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1017/wsc.2018.33zenodo-depositor-declared
Omics in Weed Science: A Perspective from Genomics, Transcriptomics, and Metabolomics Approaches
inferred← citeshttps://doi.org/10.1002/ps.5048openalex-snapshot
The power and potential of genomics in weed biology and management
inferred← citeshttps://doi.org/10.1002/ps.5128openalex-snapshot
Introduction to Pest Management Science special issue for GHRC 2017
inferred← citeshttps://doi.org/10.1002/ps.5485openalex-snapshot
Physiological and molecular analysis of glyphosate resistance in non‐rapid response Ambrosia trifida from Wisconsin
inferred← citeshttps://doi.org/10.1002/ps.5800openalex-snapshot
Identification and expression of main genes involved in non‐target site resistance mechanisms to fenoxaprop‐p‐ethyl in Beckmannia syzigachne
inferred← citeshttps://doi.org/10.1002/ps.6733openalex-snapshot
Identification of essential genes involved in metabolism‐based resistance mechanism to fenoxaprop‐ P ‐ethyl in Polypogon fugax
inferred← citeshttps://doi.org/10.1002/ps.71227openalex-snapshot
Glutathione S ‐transferase genes Pf GSTU6 and Pf GSTL1 involved in mesosulfuron‐methyl resistance in Polypogon fugax
inferred← citeshttps://doi.org/10.1002/ps.71386openalex-snapshot
First report of Quizalofop ‐p‐ethyl resistance in Eriochloa villosa involving non‐target‐site mechanisms
inferred← citeshttps://doi.org/10.1002/ps.7728openalex-snapshot
Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance
inferred← citeshttps://doi.org/10.1016/j.aquabot.2023.103631openalex-snapshot
Transcriptional responses to 2,4-D herbicide treatment of a Eurasian (Myriophyllum spicatum) and a hybrid (M. spicatum × M. sibiricum) genotype of watermilfoil that differ in their sensitivity to 2,4-D
inferred← citeshttps://doi.org/10.1016/j.pestbp.2025.106500openalex-snapshot
Characterization of Cyhalofop-butyl metabolism and identification of resistance genes in Barnyardgrass (Echinochloa crus-galli (L.) P. Beauv.)
inferred← citeshttps://doi.org/10.1016/j.plantsci.2019.110255openalex-snapshot
Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies
inferred← citeshttps://doi.org/10.1016/j.plaphy.2025.109596openalex-snapshot
A novel ACCase Trp-1999-Gly mutation confers resistance to ACCase-inhibiting herbicides in Chinese sprangletop (Leptochloa chinensis)
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2019.03.089openalex-snapshot
Unravelling mesosulfuron-methyl phytotoxicity and metabolism-based herbicide resistance in Alopecurus aequalis: Insight into regulatory mechanisms using proteomics
inferred← citeshttps://doi.org/10.1017/wsc.2021.76openalex-snapshot
Characterization and inheritance of dicamba resistance in a multiple-resistant waterhemp (Amaranthus tuberculatus) population from Illinois
inferred← citeshttps://doi.org/10.1017/wsc.2022.68openalex-snapshot
Utilization of image-based spectral reflectance to detect herbicide resistance in glufosinate-resistant and glufosinate-susceptible plants: a proof of concept
inferred← citeshttps://doi.org/10.1017/wsc.2023.73openalex-snapshot
Identification of candidate genes involved with dicamba resistance in waterhemp (Amaranthus tuberculatus) via transcriptomics analyses
inferred← citeshttps://doi.org/10.1021/acs.jafc.0c07512openalex-snapshot
Investigating the Mechanism of Metabolic Resistance to Tribenuron-Methyl in Capsella bursa-pastoris (L.) Medik. by Full-Length Transcriptome Assembly Combined with RNA-Seq
inferred← citeshttps://doi.org/10.1021/acs.jafc.2c04529openalex-snapshot
Investigating the Metabolic Mesosulfuron-Methyl Resistance in Aegilops tauschii Coss. By Transcriptome Sequencing Combined with the Reference Genome
inferred← citeshttps://doi.org/10.1021/acs.jafc.3c04323openalex-snapshot
First Report on Resistance to HPPD Herbicides Mediated by Nontarget-Site Mechanisms in the Grass Leptochloa chinensis
inferred← citeshttps://doi.org/10.1021/acs.jafc.3c05921openalex-snapshot
Target-Site and Metabolic Resistance Mechanisms to Penoxsulam in Late Watergrass (Echinochloa phyllopogon) in China
inferred← citeshttps://doi.org/10.1021/acs.jafc.4c02674openalex-snapshot
Two Cytochrome P450s, CYP709B1 and CYP704C1 , Play Essential Roles in Metabolism-Based Multiple Herbicide Resistance in American Sloughgrass ( Beckmannia syzigachne (Steud.) Fernald)
inferred← citeshttps://doi.org/10.1021/acs.jafc.5c00299openalex-snapshot
OsGSTF1 Endows Higher Tolerance of Oryza sativa to 4-Hydroxyphenylpyruvivate Dioxygenase Inhibitor Tripyrasulfone than Echinochloa crus-galli
inferred← citeshttps://doi.org/10.1021/acs.jafc.5c01785openalex-snapshot
First Report on Resistance to ALS-Inhibiting Herbicides in the Broadleaved Weed Common Vetch (Vicia sativa L.) and Visual Detection of the Associated ALS Resistance Mutation
inferred← citeshttps://doi.org/10.1021/acs.jafc.8b02740openalex-snapshot
Enhanced Herbicide Metabolism and Metabolic Resistance Genes Identified in Tribenuron-Methyl Resistant Myosoton aquaticum L.
inferred← citeshttps://doi.org/10.1021/bk-2018-1294.ch005openalex-snapshot
Use of Omics Methods To Determine the Mode of Action of Natural Phytotoxins
inferred← citeshttps://doi.org/10.1074/jbc.rev120.013572openalex-snapshot
Mechanisms of evolved herbicide resistance
inferred← citeshttps://doi.org/10.1093/gbe/evaa191openalex-snapshot
Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance
inferred← citeshttps://doi.org/10.1111/tpj.70926openalex-snapshot
PfCYP94C179 endows resistance to fenoxaprop‐ P ‐ethyl in Polypogon fugax : insights into its herbicide detoxification function and transcription regulation
inferred← citeshttps://doi.org/10.1186/s12870-023-04524-0openalex-snapshot
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.)
inferred← citeshttps://doi.org/10.1515/helia-2019-0002openalex-snapshot
Decoding Non-Target-Site Herbicide Resistance in Sunflower: The Beginning of the Story
inferred← citeshttps://doi.org/10.3389/fpls.2020.609209openalex-snapshot
Non-target-Site Resistance in Lolium spp. Globally: A Review
inferred← citeshttps://doi.org/10.3389/fpls.2021.798858openalex-snapshot
RNA-Seq Transcriptome Analysis Provides Candidate Genes for Resistance to Tomato Leaf Curl New Delhi Virus in Melon
inferred← citeshttps://doi.org/10.3389/fpls.2022.868807openalex-snapshot
Expression Pattern of Entire Cytochrome P450 Genes and Response of Defenses in a Metabolic-Herbicide-Resistant Biotype of Polypogon fugax
inferred← citeshttps://doi.org/10.3389/fpls.2024.1404889openalex-snapshot
Mapping of flumioxazin tolerance in a snap bean diversity panel leads to the discovery of a master genomic region controlling multiple stress resistance genes
inferred← citeshttps://doi.org/10.3389/fpls.2026.1870671openalex-snapshot
Dose-response-defined physiological framework enables comparative analysis of transcriptional response dynamics across multiple herbicides in Arabidopsis thaliana
inferred← citeshttps://doi.org/10.3390/agronomy13030702openalex-snapshot
Comparative Transcriptome Analysis of the Differential Effects of Florpyrauxifen-Benzyl Treatment on Phytohormone Transduction between Florpyrauxifen-Benzyl-Resistant and -Susceptible Barnyard Grasses (Echinochloa crus-galli (L.) P. Beauv)
inferred← citeshttps://doi.org/10.3390/plants13131751openalex-snapshot
Metabolism-Based Herbicide Resistance to Mesosulfuron-methyl and Identification of Candidate Genes in Bromus japonicus
inferred← citeshttps://doi.org/10.3390/plants15121908openalex-snapshot
Molecular Mechanisms of Resistance to Cyhalofop-Butyl in Barnyard Grass (Echinochloa crus-galli)
inferred← citeshttps://doi.org/10.3390/plants9060685openalex-snapshot
Transcriptome Analysis Identifies Candidate Target Genes Involved in Glyphosate-Resistance Mechanism in Lolium multiflorum
inferred← citeshttps://doi.org/10.6084/m9.figshare.24432033openalex-snapshot
Additional file 1 of 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.)
inferred← citeshttps://doi.org/10.6084/m9.figshare.24432085openalex-snapshot
Additional file 2 of 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.)
inferred← citeshttps://doi.org/10.70675/ad6e06b5z0bbbz409ezbc0az0b99311346c7openalex-snapshot
Évolution de la résistance aux herbicides chez l'Ambroisie à feuilles d'armoise (Ambrosia artemisiifolia) : recherche des déterminismes génétiques et application au diagnostic moléculaire.
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