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Microarray data from aerial tissue of Williams 82 soybean exposed to submergence and reoxygenation

ABSTRACT: Submergence is a major constraint for soybean production worldwide and transient inundation after seeding causes serious loss of soybean productivity. To characterize genome-scale adjustment of gene expression to submergence and reoxygenation, whole transcriptome analysis was conducted using Affymetrix Soybean Gene 1.0 ST Arrays.

ORGANISM(S): Glycine max

PROVIDER: GSE51710 | GEO | 2014/02/18

SECONDARY ACCESSION(S): PRJNA224688

REPOSITORIES: GEO

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Microarray data from aerial tissue of Williams 82 soybean exposed to submergence and reoxygenation

Project description:Submergence is a major constraint for soybean production worldwide and transient inundation after seeding causes serious loss of soybean productivity. To characterize genome-scale adjustment of gene expression to submergence and reoxygenation, whole transcriptome analysis was conducted using Affymetrix Soybean Gene 1.0 ST Arrays. Aerial tissue of soybean which were treated with 1 d submergence, 5 d submergence, and 5 d submergence + 1 d reoxygenation were subjected to RNA extraction and hybridization on Affymetrix microarrays (Soybean Gene 1.0 ST arrays). Non-submerged were used as control. Two independent biological replicates were analyzed for each treatment.

2014-02-18 | E-GEOD-51710 | biostudies-arrayexpress

Jasmonate Regulates Plant Responses to Reoxygenation through Activation of Antioxidant Synthesis

Project description:Submergence induces hypoxia in plants; exposure to oxygen following submergence, termed reoxygenation, produces a burst of reactive oxygen species. The mechanisms of hypoxia sensing and signaling in plants have been well studied, but how plants respond to reoxygenation remains unclear. Here, we show that reoxygenation in Arabidopsis thaliana involves rapid accumulation of jasmonates (JAs) and increased transcript levels of JA biosynthesis genes. Application of exogenous methyl jasmonate improved tolerance to reoxygenation in wild-type Arabidopsis; also, mutants deficient in JA biosynthesis and signaling were very sensitive to reoxygenation. Moreover, overexpression of the transcription factor gene MYC2 enhanced tolerance to post-hypoxic stress and myc2 knockout mutants showed increased sensitivity to reoxygenation, indicating that MYC2 functions as a key regulator in the JA-mediated reoxygenation response. MYC2 transcriptionally activates members of the VITAMIN C DEFECTIVE (VTC) and GLUTATHIONE SYNTHETASE (GSH) gene families, which encode rate-limiting enzymes in the ascorbate and glutathione synthesis pathways. Overexpression of VTC1 and GSH1 in the myc2-2 mutant suppressed the post-hypoxic hypersensitive phenotype. The JA-inducible accumulation of antioxidants may alleviate oxidative damage caused by reoxygenation, improving plant survival after submergence. Taken together, our findings demonstrate that JA signaling interacts with the antioxidant pathway to regulate reoxygenation responses in Arabidopsis.

2017-08-25 | GSE93393 | GEO

Microarray data from aerial tissue of submergence tolerant M202(Sub1) and intolerant M202

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.

2010-02-04 | GSE18930 | GEO

Microarray data from aerial tissue of submergence tolerant M202(Sub1) and intolerant M202

2010-02-22 | E-GEOD-18930 | biostudies-arrayexpress

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

Project description:Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence.

2015-01-01 | GSE63429 | GEO

Glycine max cultivar:Williams 82

Project description:Soybean snRNA-seq

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Studies of autophagy pathway during submergence in Arabidopsis thaliana

Project description:Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. To study the role of autophagy during submergence, we performed transcriptome analysis with atg5, an autophagy-defective mutant, under submergence conditions. Our data showed that submergence changed the expression profile of DEG in the atg5 versus wild-type.

2021-09-20 | GSE184340 | GEO

Construction of gene expression profiles for anoxia-reoxygenation in Arabidopsis

Project description:To understand how plants respond to anoxia-reoxygenation, we have employed a global microarray expression profiling as a basic platform to characterize genes with the potential to mediate the recovery responses in Arabidopsis. 7-day-old seedlings were trated with 4hr and 8hr anoxia, and then reoxygenated in air for 0, 0.5, 1, 3, 6 hrs. Genes changed in both condition were designated as reoxygenation-regulated genes. They included the genes in ROS detoxification, dehydration, metabolic process, and many other responses. Interestingly, ethylene was also involved in this recovery process. We further adopted ein2-5 and ein3eil1 microarray to investigate ethylene signaling. Our results showed ethylene partially regulate reoxygenation regulated genes and is reruired for plant survival in reoxygenation. Genes expression during anoxia-reoxygenation in Arabidopsis seedlings was measured at 0, 0.5, 1, 3, 6 hours after anoxia treatment, and normal condition before anoxia. Three independent experiments were performed at each time (Nor, 0, 0.5, 1, 3, 6) under 4hr anoxia-reoxygenation condition by using Col-0, ein2-5, and ein3eil1. Four independent experiments were performed at each time (Nor, 0, 0.5, 1, 3, 6) under 8hr anoxia-reoxygenation condition by using Col-0.

2014-02-18 | E-GEOD-51767 | biostudies-arrayexpress

Down-regulation of NDRG1 promotes migration of cancer cells during reoxygenation

Project description:To investigate the transcriptional response of tumor adaptation to reoxygenation, breast cancer cells MCF-7 was cultured under 0.5% of hypoxia for 24h followed by 24h of reoxygenation in normoxia. Cells were harvested respectively at 0, 1, 4, 8, 12, and 24h during reoxygenation. Total RNA obtained from human breast cancer cell line MCF-7 were collected respectively at 0, 1, 4, 8, 12 and 24 hours after reoxygenation.

2012-01-01 | E-GEOD-30019 | biostudies-arrayexpress

Quantitative Phosphoproteomics Reveals Targets of Protein Kinase SnRK1 in Arabidopsis under Submergence

Project description:SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed as a central integrator of regulatory pathways in plant stress and energy starvation signaling. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. To gain further insight into submergence signaling mechanisms, we determined the temporal response to energy starvation through AMP/ATP quantification and used quantitative phosphoproteomics to compare the global changes in phosphopeptides in Col-0 and SnRK1.1K48M. We found that the phosphorylation levels of 59 peptides increased and the levels of 96 peptides decreased in Col-0 within 0.5–3 h of submergence. Among the 59 peptides with increased phosphorylation in Col-0, 49 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved in sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. In particular, the phosphorylation of MAPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MAPK6 activity that directly dephosphorylates MAPK6, was also regulated by SnRK1.1. These results reveal insights into the function of SnRK1 and the downstream signaling factors of submergence.

2016-04-07 | PXD001815 | Pride

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