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ABSTRACT:
PROVIDER: PRJNA839759 | ENA |
REPOSITORIES: ENA
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Project description:Multiple herbicide resistance in Palmer amaranth (Amaranthus palmeri S. Watson) poses a serious threat to US crop production. A Palmer amaranth population (KCTR) from Kansas was found resistant to herbicides across six sites of action, including ALS-, PS II-, EPSPS-, PPO-, HPPD-inhibitors and synthetic auxins. Moreover, a predominance of metabolic resistance, possibly mediated by P450s or GSTs enzyme activity was reported in this population. This study aims to identify the specific genes involved in multiple herbicide metabolism in this Palmer amaranth population via transcriptome analysis. Vegetative clones were developed from three biological replicates of both resistant (KCTR/KCTR-G2) and susceptible (KSS) Palmer amaranth populations. Ten to 12 cm tall clones from each biological replicate were treated with labelled doses of chlorsulfuron, 2,4-D, atrazine, lactofen and mesotrione. Leaf samples were collected for RNA isolation at 6 hours after treatment with respective herbicides along with non-treated plants. Upon RNA sequencing, paired end reads generated were mapped to the Palmer amaranth transcriptome using HISAT2. Differential gene expression analysis revealed 414, 129, 529, 688 and 152 genes expressed differentially in resistant plants following chlorsulfuron, 2,4-D, atrazine, lactofen and mesotrione treatments, respectively. Isoforms of CYP72A219 or CYP704B1 and GST C-terminal were alternatively up-regulated expression across treatments. Transcripts for CYP72A219 and CYP704B1 show up-regulated expression of 3.4- to 6.6-fold and 5.9- to 12.4-fold in resistant plants as validated by qRT-PCR. Identification of genes involved in multiple herbicide metabolism in Palmer amaranth is crucial to predict the evolutionary course of herbicide resistance in weed species.
2026-04-07 | GSE326567 | GEO
Project description:Metabolism of the 4-hydroxyphenylpyruvate dioxygenase-inhibiting herbicide mesotrione in two resistant vs two sensitive Palmer amaranth (Amaranthus palmeri) populations analysed via LC-MS based untargeted metabolomics of excised leaf extracts harvested for each population across five time points (2, 4, 8, 12 and 24 hrs).
2023-06-30 | MSV000092317 | MassIVE
Project description:CYP72A1182 is involved in metabolic resistance evolution to tembotrione in Palmer amaranth
| PRJNA1016406 | ENA
Project description:Giant ragweed (Ambrosia trifida) is an economically disruptive weed in US corn and soybean production. Populations of this species have evolved a unique glyphosate resistance mechanism involving rapid cell death in mature leaves, also known as rapid necrosis. This abiotic stress resistance mechanism may be due to utilization of stress response pathways typically associated with biotic stresses such as pathogens. To study the genetic basis of this rapid response, an RNA-Seq time course study was conducted on young and mature leaves of glyphosate-resistant and -susceptible individuals, before and after glyphosate treatment. A major difference in gene regulation following glyphosate application was observed between young and mature leaves in the glyphosate-resistant individuals. Many differentially expressed genes were related to broad plant pathways with cross-functionality including plant stress and cell death pathways, phytohormone synthesis, response to oxidative stress, cellular metabolism, and pathogen defense pathways. Metabolic network analysis revealed that most of the genes involved in jasmonate biosynthesis were up regulated in response to glyphosate treatment in resistant mature leaves whereas this pathway was not induced in susceptible plants. The glyphosate-resistant plants appear to perceive glyphosate differently than susceptible plants, pointing to the potential role of a yet to be characterized receptor that senses glyphosate or its action and triggers the rapid necrosis response in mature leaves. Additional steps are needed for functional validation to test the hypothesis of causal relationship between function of these candidate genes of interest and the glyphosate resistance rapid response phenotype.
2025-12-31 | GSE150914 | GEO
Project description:Background: Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new glyphosate-tolerant varieties is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire otherglyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice. Results: Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg•ml-1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L+1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L+1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1). Conclusion: Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate stress in rice.
2020-03-23 | GSE142110 | GEO
Project description:Metabolism of the 4-hydroxyphenylpyruvate dioxygenase-inhibiting herbicide mesotrione in two resistant vs two sensitive Palmer amaranth (Amaranthus palmeri) populations analysed via LC-MS based untargeted metabolomics of excised leaf extracts harvested for each population across five time points (2, 4, 8, 12 and 24 hrs).
2023-06-30 | MSV000092317 | GNPS
Project description:Deciphering Metabolic Resistance to Multiple Herbicides in Palmer amaranth (Amaranthus palmeri S. Watson) via Transcriptome Analysis
| PRJNA1445906 | ENA
Project description:Using whole genome microarray (Affymetrix ATH1) we studied the transcriptional response of Arabidopsis thaliana to glyphosate (Roundup Original) herbicde that inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme and thus disrupts aromaticamino acid biosynthesis. Few genes related to defense and secondary metabolism were altered. Experiment Overall Design: Surfactant (preference 0.25%) treated plants were used as carrier control group and EC50 concentration of glyphosate was used as the herbicide treatment group. Each of the control and treatment group consisted of 3 biological replicates and each biological replicates comprised leaves from 10 individual plants. RNA was extracted at 24h post treatment to study the transcriptional alterations caused by the herbicide treatment.
2009-08-07 | E-GEOD-8927 | biostudies-arrayexpress
Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course following glyphosate treatments where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were not treated with glyphosate (Series GSE71321). 3) A previously submitted study of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course following a glyphosate treatment study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).
2015-08-05 | E-GEOD-71406 | biostudies-arrayexpress
Project description:Small RNAs have emerged as a promising new type of biomarker to monitor health status and track the development of diseases. Here we report changes in the levels of small RNAs in the liver of rats exposed to a mixture (MIX) of six pesticides frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole), and glyphosate (G50) (50 mg/kg bw/day), or its representative EU commercial herbicide formulation Roundup MON 52276 (R50) at the same glyphosate equivalent doses in comparison to a control group (CON).
2022-03-09 | GSE182559 | GEO