Differential expression of genes involved in salt-treated iU1 seedlings
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ABSTRACT:
PROVIDER: PRJNA798070 | ENA |
REPOSITORIES: ENA
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Project description:To help understanding the mechanisms involved in the development of salt hypersenstivitivy phenotype of iU1 seedlings.
2022-06-29 | GSE193841 | GEO
Project description:Purpose: The goals of this study are to compare differentially expressed transcripts in seedlings of watermelon during salt stress using transcriptome profiling (RNA-seq)
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Project description:To gain insight into how AtCAPE1 regulates salt response, we investigated the gene expression profiles of wild-type (Ler) and proatcape1 mutant seedlings in the presence and absence of 125 mM NaCl by microarray analysis.
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Project description:The Fusarium incarnatum strain K23, originally isolated from a habit-adapted wild plant Thapsia species, colonized the roots and shoots of tomato seedlings and protected them against salt stress. Comparison of expression and metabolite profile changes uncovered that the fungus completely reprogramed the tomato response to salt stress. Barely any overlap was observed among the genes and metabolites which are regulated by salt stress in uncolonized and colonized tomato seedlings. In colonized seedlings exposed to salt stress, less stress- related genes are activated than in un-colonized seedlings. Furthermore, K23 produced gibberellin and gibberellin-responsive genes were detected in all RNA samples. Our analysis demonstrates that K23 colonisation completely alters the salt-responsive gene and metabolite profiles in tomato seedlings.
2024-11-30 | GSE255960 | GEO
Project description:Large-scale gene expression affected by salt stress was analyzed with tomato seedlings (Lycoperson esculentum Mill cv. Money Maker) by a cDNA microarray (Tom1). The significantly differentially expressed genes (5% Benjamini-Hochberg false discovery rate) consisted of 1757 sequences in the analyzed tissues (cotyledons + shoot tip). Genes with over 2 fold difference were selected from the list and further categorized into different function and cellular processes. Tomato homologous genes for the chaperone proteins, antioxidant enzymes (catalase and peroxidase), and ion transporters (Na+-driven multidrug efflux pump, vacuolar ATPase, and others) were induced. The ACC oxidase and ethylene-responsive gene tomato homologs had higher transcript level after salt treatment. Multiple members with different expression patterns were identified for the bZIP, WRKY, and MADS-box transcription regulator. Different genes in the signal transduction pathway, such as the protein kinases (Shaggy kinase, mitogen-activated protein kinase, ethylene receptor neverripe, and others), protein phosphatases, calmodulin, G-protein, and the N- myristoyltransferase, were regulated by salt stress. Most of the protease and the inhibitor homologs were suppressed by salt stress. In addition, different isoforms of cytochrome P450, genes for polyamine biosynthesis (putrescine and proline) and detoxification compounds (glutathione and thioredoxin), several key enzyme genes in the metabolic pathways of carbohydrates, amino acids, and fatty acids, were also affected by salt treatment. This study has provided a set of candidate genes, especially those in the regulatory machinery that can be further investigated to define salt stress in tomato and other plant species. Keywords: treatment response
2007-09-05 | GSE8883 | GEO
Project description:To gain insight into how AtCAPE1 regulates salt response, we investigated the gene expression profiles of wild-type (Ler) and proatcape1 mutant seedlings in the presence and absence of 125 mM NaCl by microarray analysis. Ten seedlings were grown vertically on the mesh attached on 1/2 MS medium for 10 days. Seedlings with the mesh were transferred to a new petri dish and then covered by buffer-saturated filter papers with 1/2 MS liquid medium (Control) or with 125 mM NaCl (Salt). Salt-treated seedlings (n=10 for each treatment) were sampled after 12 h. Three independent experiments were performed for the microarray analysis.
2015-07-01 | E-GEOD-66946 | biostudies-arrayexpress
Project description:Large-scale gene expression affected by salt stress was analyzed with tomato seedlings (Lycoperson esculentum Mill cv. Money Maker) by a cDNA microarray (Tom1). The significantly differentially expressed genes (5% Benjamini-Hochberg false discovery rate) consisted of 1757 sequences in the analyzed tissues (cotyledons + shoot tip). Genes with over 2 fold difference were selected from the list and further categorized into different function and cellular processes. Tomato homologous genes for the chaperone proteins, antioxidant enzymes (catalase and peroxidase), and ion transporters (Na+-driven multidrug efflux pump, vacuolar ATPase, and others) were induced. The ACC oxidase and ethylene-responsive gene tomato homologs had higher transcript level after salt treatment. Multiple members with different expression patterns were identified for the bZIP, WRKY, and MADS-box transcription regulator. Different genes in the signal transduction pathway, such as the protein kinases (Shaggy kinase, mitogen-activated protein kinase, ethylene receptor neverripe, and others), protein phosphatases, calmodulin, G-protein, and the N- myristoyltransferase, were regulated by salt stress. Most of the protease and the inhibitor homologs were suppressed by salt stress. In addition, different isoforms of cytochrome P450, genes for polyamine biosynthesis (putrescine and proline) and detoxification compounds (glutathione and thioredoxin), several key enzyme genes in the metabolic pathways of carbohydrates, amino acids, and fatty acids, were also affected by salt treatment. This study has provided a set of candidate genes, especially those in the regulatory machinery that can be further investigated to define salt stress in tomato and other plant species. Keywords: treatment response Effect of 75mM NaCl on gene’s expression in tomato seedlings, Lycoperscon esculentum Mill. cv. Money Maker after 17 d of treatment. Each sample represents a pool of same tissue 20 seedlings grown in two flasks. Experiment was done in triplicate.
2007-09-04 | E-GEOD-8883 | biostudies-arrayexpress
Project description:A tandem mass tag (TMT)-based comparative peptidomics analysis of rice seedlings under salt stress was conducted. Rice seedlings were exposed to 50 and 150 mM NaCl for 24 and 72 h, respectively, and the root and shoot tissues of different treatment groups were collected separately for the peptidomic analysis.
2023-03-11 | PXD037574 | Pride
Project description:Ice plant (Mesembryanthemum crystallinum L.) is a halophyte and an inducible CAM plant. Ice plant seedlings exhibit moderate salt tolerance, with root growth unaffected by 200 mM NaCl treatments, while hypocotyl elongation is hindered in salt-stressed etiolated seedlings. Superoxide anion accumulation was prominent in cotyledons and primary leaves but decreased in root tissues over time but was not significantly affected by salt treatment. Hydrogen peroxide (H2O2) levels surged initially in both control and salt-treated seedlings, with higher and more persistent H2O2 levels in salt-treated seedlings, indicating salt-induced ROS accumulation, especially in etiolated seedlings. An RNA-seq analysis of etiolated seedlings revealed 6,326 unigenes (about 8%) showing more than a four-fold change in expression after a 6-h 200 mM NaCl treatment. The top GO terms for 4-fold upregulated DEGs in the Molecular Function category included “cation binding,” “metal ion binding,” “oxidoreductase activity,” “monooxygenase activity,” and “antioxidant activity.” The top GO terms for 4-fold down-regulated DEGs in the Biological Process category included “metabolic process”, “cellular metabolic process”, and “biosynthetic process”. Upregulated genes were primarily linked to ion transport and stress responses and downregulated genes to growth processes like ribosomal protein synthesis and cell wall formation. This indicates that salt stress hinders growth but enhances ion homeostasis and stress response mechanisms. For class III peroxidase family genes, 14 out of 53 identified transcripts met the criteria for differentially expressed genes. Quantitative RT-PCR confirmed that the expression of McPrx4.1, McPrx12.1, and McPrx12.3 increased, while the expression of McPrx60.3 decreased. We suggest distinct roles for individual class III peroxidase members in the trade-offs between plant growth and stress response. Unveiling these responses will advance our understanding of the growth–stress balance in the intrinsic salt tolerance in halophytes.
2025-01-01 | GSE277109 | GEO
Project description:High salinity is one of the most serious threats to crop production. To 1 better understand the molecular basis of plant responses to salt stress, we combined suppression subtractive hybridization (SSH) and microarray approaches to identify the potential important or novel genes involved in salt tolerance. First, SSH libraries were constructed for two cultivated tomato (Solanum lycopersicum) genotypes: LA2711, a salt tolerant cultivar, and ZS-5, a salt sensitive cultivar, to compare salt treatment and non-treatment plants. Then a subset of clones from these SSH libraries were used to construct a tomato cDNA array and microarray analysis was carried out to verify the expression changes of this set of clones upon salt treatment at various time points compared to the corresponding non-treatment controls. A totalof 201 non-redundant genes differentially expressed upon 30 min of salt stress treatment either in LA2711 or ZS-5 were identified from microarray analysis, most of which were not previously associated with salt stress. The diversity of the putative functions of these genes indicated that salt stress resulted in a complex response in tomato plants. Keywords: gene expression, genotype, microarray, salt stress, SSH, tomato
2007-01-09 | GSE4961 | GEO