Flood tolerant Cardamineae
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB73992 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Rsyl_trans.fasta.gz | Fasta.gz | |||
| Rpal_trans.fasta.gz | Fasta.gz | |||
| Cpra_trans.fasta.gz | Fasta.gz | |||
| Chir_trans.fasta.gz | Fasta.gz |
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Project description:RNAseq of submergence response of the flood tolerant Cardamineae tribe
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Project description:Pot grown plants of Arabidopsis thaliana, Cardamine hirsuta, Cardamine pratensis, Rorippa palustris and Rorippa sylvestris where completely submerged under ambient light conditions. After 24 and 48 hours the shoots were harvested for expression analysis. Differential expression analysis, taking into account unsubmerged control plants revealed that the Rorippa genus had a pronounced down regulation of the cell cycle whereas the Cardamine had an attenuated response to submergence.
2024-04-01 | E-MTAB-13910 | biostudies-arrayexpress
Project description:Waterlogging and submergence are major abiotic stresses impairing rapeseed development and hence evaluation of waterlogging tolerance ability is crucial for the development of tolerant lines through breeding approaches. This study investigated submergence impact on the survival rate, physiological responses, and transcriptomic variation of the young seedlings of 706 Brassica napus germplasm. We identified 57 highly tolerant and 109 highly susceptible accessions underwent six days submergence. Most accessions originated from the downstream of Yangtze River region had higher tolerance level. SOD enzymic activity increased both in the five representative tolerant and susceptible genotypes under submergence stress. POD activity also increased in the tolerant genotypes whereas CAT activity decreased, showing a opposite trend compared to the susceptible genotypes. The tolerant genotypes showed less chlorosis and produced less malondialdehyde than that in the susceptible group, while soluble protein content increased more than that in the susceptible genotypes. Transcriptome analysis detected 5,072 and 5,063 up-regulated genes, as well as 3,512 and 3,889 down-regulated genes in the tolerant / susceptible group in comparison to their respective control. Many genes encoding the transcription factors in AP2/ERF, bHLH, MYB, WRKY, and NAC families were also significantly regulated. The differentially expressed genes shared by the two pairs comparison were mainly enriched in such KEGG pathways as circadian rhythm, tryptophan metabolism, and porphyrin and chlorophyll metabolism. The specific pathways in the tolerant group were enriched in carbon metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acid etc. while the specific pathways in the susceptible group were more distributed in hormone signal transduction, sucrose and starch metabolism, and vitamin B6 metabolism etc. The results uncovered distinct physiological and transcriptomic differences between tolerant and susceptible genotypes.
2025-12-26 | GSE314699 | GEO
Project description:Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation. Keywords: Abiotic stress tolerance response
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Project description:Leaf age determines flood resilience through distinct submergence and recovery effects
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Project description:Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting crop performance and yield. While the response of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, we hardly know anything about the response of its relative, the important oil crop plant Brassica napus. Here, we analyzed the molecular response of leaves of rapeseed seedlings to full submergence under illumination. RNAseq experiments revealed a strong carbon starvation response under submergence, but no indication for a low-oxygen response. We used two cultivars in this study, one Asian flooding-tolerant cultivar and one European hybrid cultivar, but those genotypes did not show strong differences in their responses to submergence.
2020-10-28 | GSE140828 | GEO
Project description:Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation. Keywords: Abiotic stress tolerance response Three-condition experiment, M202(Sub1) vs wild type control (M202) at three durations of submergence (0d, 1d and 6d). Biological replicates: 2, independently grown and harvested. Technical replicates replicates: 1-2 control.
2010-03-08 | E-GEOD-17704 | biostudies-arrayexpress
Project description:In plants, programmed cell death (PCD) is involved in both the development and in the response to biotic and abiotic aggressions. In early stages of PCD, mitochondrial membranes are made permeable by the formation of permeability transition pores, whose protein composition is debated. Since flooding stress can produce PCD in several plant species, the first goal of this work was to know if flooding stress could be used to induce PCD in Beta vulgaris roots. To do this, two months old beet plants were flood-stressed from one to five days, and the alterations indicating PCD in stressed beetroot cells were observed with a confocal fluorescence microscope. In addition, cytochrome c was released from mitochondria. After assessing that flood stress induced PCD in beetroots, the composition of mitochondrial protein complexes was observed in control and flood-stressed beetroots. Protein complexes from isolated mitochondria were separated by native gel electrophoresis, and their proteins were identified by mass spectrometry. The spectra count of three isoforms of voltage-dependent anion-selective channels (VDAC) increased after one day of flooding. In addition, the size of the complexes formed by VDAC was higher in beetroots flood-stressed for one day (~200 kDa) compared with non-stressed ones (~100 kDa). Other proteins, like chaperonin CPN60-2, also formed complexes with different masses in control and flood-stressed beetroots. Finally, possible interactions of VDAC with other proteins were found performing a cluster analysis. These results indicate that mitochondrial protein complexes formed by VDAC could be involved in the process of programmed cell death in flood-stressed beetroots
2021-10-28 | PXD027781 | Pride
Project description:An ERF transcription factor, Submergence-1A (Sub1A), dramatically enhances the tolerance to prolonged submergence in rice. For instance, rice accessions which lack Sub1A (e.g. M202) die within 7-10 d of complete submergence. By contrast, genotypes which posses Sub1A (e.g. M202(Sub1)) can endure submergence stress for 14 d. In this study, the two near isogenic lines with and without Sub1A were subjected to microarray analysis using Affymetrix Gene Chip technology. This analysis provided beneficial information to elucidate general response to submergence stress and to estimate Sub1A-dependent defense response to the stress at mRNA accumulation level.
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Project description:In rice (Oryza sativa L.), the haplotype at the multigenic SUBMERGENCE 1 (SUB1) locus determines survival of prolonged submergence. SUB1 encodes two or three group VII Ethylene Response Factor (ERF) family transcription factors, SUB1A, SUB1B and SUB1C. A highly submergence-inducible SUB1A allele is present in lines that are submergence tolerant. This gene is the determinant of submergence tolerance. Here, the heterologous ectopic expression of rice SUB1A and SUB1C in Arabidopsis thaliana was employed to assess the transcriptional network mobilized by ectopic expression of SUB1A and SUB1C.
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