Seed color F2 GBS amaranth
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB30533 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Gene transcription in epididymal fat pads was investigated in an F2 cross of 129S6 x Balb/c mice using Illumina gene expression arrays. Expression data was determined in 5 months old male mice fed a carbohydrate diet. Genotyping data for the F2 offspring used in this study can be found in the file E-MTAB-395.additional.zip under the Browse all available files link (file mouse-f2-chd-genotype.txt added 8th April 2014).
2014-01-20 | E-MTAB-395 | biostudies-arrayexpress
Project description:Anterior pituitary glands were isolated from 21 week old male rats treated for 12 weeks with the synthetic estrogen diethylstilbestrol (DES). 43 COPxACI F2 animals were selected based on pituitary weight phenotypic extremes: 22 highest and 21 lowest pituitary weights in our F2 population. Expression profiles were determined using Affymetrix Rat Genome 230 v. 2.0 arrays. In conjunction with genomewide genotypes available for these 43 animals, linkage analysis was done using mRNA abundance of each transcript on the array as a separate quantitative phenotype. These arrays provide a resource for expression QTL (eQTL) mapping on a genomewide level in the pituitary gland. Experiment Overall Design: 43 samples from anterior pituitary gland were analyzed. COPxACI F2 male animals were treated with DES for 12 weeks, starting at 9 weeks of age. Pituitary glands were harvested and weighed at sacrifice (21 weeks of age). The 43 samples were selected for pituitary weight phenotypic extremes: 22 highest and 21 lowest pituitary weights in our F2 population. Genomewide genotypes are available for these animals and in conjunction with the array data, genomewide expression QTL (eQTL) mapping was done.
2008-06-12 | E-GEOD-4081 | biostudies-arrayexpress
Project description:Anterior pituitary glands were isolated from 21 week old male rats treated for 12 weeks with the synthetic estrogen diethylstilbestrol (DES). 43 COPxACI F2 animals were selected based on pituitary weight phenotypic extremes: 22 highest and 21 lowest pituitary weights in our F2 population. Expression profiles were determined using Affymetrix Rat Genome 230 v. 2.0 arrays. In conjunction with genomewide genotypes available for these 43 animals, linkage analysis was done using mRNA abundance of each transcript on the array as a separate quantitative phenotype. These arrays provide a resource for expression QTL (eQTL) mapping on a genomewide level in the pituitary gland. Keywords: Estrogen Response
2006-03-31 | GSE4081 | GEO
Project description:Isoform-resolved genome annotation enables mapping of tissue-specific betalain regulation and anthocyanin regulator co-option in amaranth
| PRJEB65083 | ENA
Project description:Abiotic stress triggered by Drought or soil salinity impacts negatively on crop production. To better understand amaranth responses to those environmental stresses, transcriptomics approaches were applied to investigate changes at molecular level in leaves of two Amaranthus species: A. hybridus, a wild species that grows in saline soils and A. hypochondriacus, the most cultivated species for grain production. Under control conditions, A. hybridus showed up-regulation of organic hydroxyl and sulfur compound processes, while A. hypochondriacus showed up-regulation of genes related to photosynthetic process, amino acids, fatty acids, and secondary metabolism. Under salt stress, significantly fewer DEGs were observed in A. hybridus, interestingly those were related to phosphonate and phosphinate metabolism, phosphorous mobilization, and steroid biosynthesis. In contrast, A. hypochondriacus response to salt stress was characterized by starch, sucrose, and trehalose metabolism, porphyrin, monoterpenoid and organonitrogen compounds biosynthetic process.Under water deficit, both species showed similar transcriptional response by up-regulation of LEAs, dehydrins, and genes related to the biosynthesis of Raffinose Family Oligosaccharides. A. hypochondriacus better adaptation to grow under drought and salt stress could be due to its fast response observed by the up-regulation of MAPK signaling pathways, ABC transporters, and production of defense compounds such as glucosinolates. The common response in both amaranth species to both type of stresses was observed by modulation of secondary metabolism, which was directed towards cell wall modification, cuticle and wax metabolism, and the production of antimicrobial and antifungal metabolites
2026-01-29 | GSE288330 | GEO
Project description:Genotyping-by-sequencing of a 2HL Hvb F2 mapping population
| PRJEB5084 | ENA
Project description:Gene expression data of micro RNA from skeletal muscle samples of F2 population based DL and Pi F2 63 days post conception (dpc).
2021-08-31 | GSE162755 | GEO
Project description:Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)
| PRJEB13013 | ENA