Gene expression study after 3 days of cold or salt exposure in a Solanum tuberosum cultivar called Desirée
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum tuberosum
PROVIDER: GSE34118 | GEO | 2011/12/03
SECONDARY ACCESSION(S): PRJNA149869
REPOSITORIES: GEO
Similar Datasets
Project description:The molecular response to salt exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed, whereas cell rescue and transcription factor-related genes were mostly up-regulated. A strong down-regulation of several functional categories including primary metabolism, detoxication apparatus and signal transduction was also observed.
2011-12-03 | GSE34116 | GEO
Project description:The molecular response to cold exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon cold exposure in Desirée leaves were observed in the photosynthesis-related genes, which were down-regulated, whereas cell rescue, detoxication and transcription factor-related genes were mostly up-regulated. We also observed an increased expression of polyamine and proline synthesis-related genes, as well as some carbohydrate-related genes such as sucrose synthase and trehalose-6-phosphate synthase.
2011-12-03 | GSE34110 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE34110: Gene expression study after 3 days of cold exposure in a Solanum tuberosum cultivar called Desirée GSE34116: Gene expression study after 3 days of salt exposure in a Solanum tuberosum cultivar called Desirée Refer to individual Series
2011-12-03 | E-GEOD-34118 | biostudies-arrayexpress
Project description:The molecular response to salt exposure was studied in the leaves of a S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed. On the other hand, we observed the induction of various kinds of transcription factors implicated in osmotic stress response via ABA-dependent or ABA-independent pathways but also in plant defense pathways. This revealed a crosstalk between abiotic and biotic stress responses during salt exposure, which activated several adaptation mechanisms including HSP, LEA, dehydrins and PR proteins. Gene expression changes related to carbohydrate and amino acid metabolism were also observed, pointing at putative modifications at the metabolic level.
2009-09-11 | GSE18053 | GEO
Project description:The molecular response to cold exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon cold exposure in Desirée leaves were observed in the photosynthesis-related genes, which were down-regulated, whereas cell rescue, detoxication and transcription factor-related genes were mostly up-regulated. We also observed an increased expression of polyamine and proline synthesis-related genes, as well as some carbohydrate-related genes such as sucrose synthase and trehalose-6-phosphate synthase. Gene expression was followed at day 3 after the beginning of the treatment: cold (4°C) and control conditions. For each condition, 4 independent biological replicates were sampled.
2011-12-03 | E-GEOD-34110 | biostudies-arrayexpress
Project description:The molecular response to salt exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed, whereas cell rescue and transcription factor-related genes were mostly up-regulated. A strong down-regulation of several functional categories including primary metabolism, detoxication apparatus and signal transduction was also observed. Gene expression has been followed three days after salinity treatment (150 mM NaCl). For each condition, 4 independent biological replicates were sampled. Dye-swaps were performed.
2011-12-03 | E-GEOD-34116 | biostudies-arrayexpress
Project description:The molecular response to salt exposure was studied in the leaves of a S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed. On the other hand, we observed the induction of various kinds of transcription factors implicated in osmotic stress response via ABA-dependent or ABA-independent pathways but also in plant defense pathways. This revealed a crosstalk between abiotic and biotic stress responses during salt exposure, which activated several adaptation mechanisms including HSP, LEA, dehydrins and PR proteins. Gene expression changes related to carbohydrate and amino acid metabolism were also observed, pointing at putative modifications at the metabolic level. Gene expression has been followed at two different time-points (one and three day after salinity treatment) and conditions: salt-treatment (150 mM NaCl) and control conditions. For each time-point and conditions 3 independent biological replicates were sampled.
2010-05-05 | E-GEOD-18053 | biostudies-arrayexpress
Project description:Gradients in the elemental composition of a potato leaf tissue (i.e. its ionome) can be linked to crop potential. Because the ionome is a function of genetics and environmental conditions, practitioners aim at fine-tuning fertilization to obtain an optimal ionome based on the needs of potato cultivars. Our objective was to assess the validity of cultivar grouping and predict potato tuber yields using foliar ionomes. The dataset comprised 3382 observations in Québec (Canada) from 1970 to 2017. The first mature leaves from top were sampled at the beginning of flowering for total N, P, K, Ca, and Mg analysis. We preprocessed nutrient concentrations (ionomes) by centering each nutrient to the geometric mean of all nutrients and to a filling value, a transformation known as row-centered log ratios (clr). A density-based clustering algorithm (dbscan) on these preprocessed ionomes failed to delineate groups of high-yield cultivars. We also used the preprocessed ionomes to assess their effects on tuber yield classes (high- and low-yields) on a cultivar basis using k-nearest neighbors, random forest and support vector machines classification algorithms. Our machine learning models returned an average accuracy of 70%, a fair diagnostic potential to detect in-season nutrient imbalance of potato cultivars using clr variables considering potential confounding factors. Optimal ionomic regions of new cultivars could be assigned to the one of the closest documented cultivar.
| S-EPMC7069643 | biostudies-literature
Project description:St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species.
2011-05-01 | GSE22449 | GEO
Project description:Potato (Solanum tuberosum L.) is an important staple food worldwide. However, its growth has been heavily suppressed by salt stress. The molecular mechanisms of salt tolerance in potato remain unclear. It has been shown that the tetraploid potato Longshu No. 5 is a salt-tolerant genotype. Therefore, in this study we conducted research to identify salt stress response genes in Longshu No. 5 using a NaCl treatment and time-course RNA sequencing. The total number of differentially expressed genes (DEGs) in response to salt stress was 5508. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, it was found that DEGs were significantly enriched in the categories of nucleic acid binding, transporter activity, ion or molecule transport, ion binding, kinase activity and oxidative phosphorylation. Particularly, the significant differential expression of encoding ion transport signaling genes suggests that this signaling pathway plays a vital role in salt stress response in potato. Finally, the DEGs in the salt response pathway were verified by Quantitative real-time PCR (qRT-PCR). These results provide valuable information on the salt tolerance of molecular mechanisms in potatoes, and establish a basis for breeding salt-tolerant cultivars.
| S-EPMC7096413 | biostudies-literature