Omics · study · 2026
Deciphering Metabolic Resistance to Multiple Herbicides in Palmer amaranth (Amaranthus palmeri S. Watson) via Transcriptome Analysis
Listed in NCBI GEO
Multiple herbicide resistance in Palmer amaranth (Amaranthus palmeri S. Watson) poses a serious threat to US crop production.
Description
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.
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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.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE326nnn/GSE326567 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE326567 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1445906 ncbi.nlm.nih.gov/bioproject/PRJNA1445906 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE326567 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |