Glycine max
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA274347 | ENA |
REPOSITORIES: ENA
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Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used.
2015-07-02 | GSE65553 | GEO
Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used. The Williams 82 and DT2008 soybean plants were grown for 14 days in the vermiculite soil under greenhouse conditions. The whole plants of 14-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 10 h. All roots of independent 14-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.
2015-07-02 | E-GEOD-65553 | biostudies-arrayexpress
Project description:Two alfalfa varieties, 'Chilean' (M. sativa ssp. sativa var. Chilean, drought sensitive) and 'Wisfal' (M. sativa ssp. falcata var. Wisfal, drought tolerant), with contrasting water use efficiency were subjected to water withholding for 11 days followed by re-watering. Samples were taken for well-watered plants and plants after five, eight, eleven days of drought stress as well as plants after recovery for one day following drought stress. Roots and shoots were sampled and analyzed separately by expression profiling using Affymetrix Medicago GeneChip.
2011-08-29 | E-MEXP-3320 | biostudies-arrayexpress
Project description:Two cultivars of sorghum were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. These data are the methanol/water metabolite fraction obtained from a Folsh extraction from Sorghum bicolor leaves and roots. The metabolites were derivatized and analyzed via GC-MS at PNNL. Analyses represent the metabolite profile collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought.
2017-10-23 | MSV000081639 | MassIVE
Project description:Plants remember what they have experienced and are thereby able to confront repeated stresses more promptly and strongly. A subset of genes showed increased transcript levels under drought stress conditions, followed by a return to basal levels during recovery (watered) states, and then displayed elevated levels again under subsequent drought conditions. To screen for a set of drought stress memory genes in soybean (Glycine max L. cv. Daepoong), we designed a 180K DNA chip comprising 60-bp probes synthesized in situ to examine 55,588 loci. Through microarray analysis using the DNA chip, we identified 2,165 and 2,385 genes with more than 4-fold increases or decreases in transcript levels, respectively, under initial (first) drought stress conditions, when compared with the non-treated control. The transcript levels of the genes returned to basal levels during recovery (watered) states, then 677 and 987 genes displayed more than 16-fold elevated or reduced levels, respectively, under subsequent (second) drought conditions, when compared to the non-treated control. Gene Ontology analysis classified the drought stress memory genes into several functional categories, including those involved in trehalose biosynthesis and drought tolerance responses. We selected a number of drought stress memory genes encoding various transcription factors, protein phosphatase 2Cs, and late embryogenesis abundant proteins, and confirmed the microarray data by quantitative reverse-transcription real-time PCR. Upon repeated watering and subsequent (third) drought treatment, the elevated levels of the drought stress memory gene transcripts were propagated into newly developed second leaves, although at reduced levels when compared to the second drought treatment on the first leaves.
2020-07-13 | GSE153660 | GEO
Project description:The isotopic dimethyl labeling-based quantitative post-translational modification proteomics was applied to study the phosphoproteomic changes associated with the drought responses of two contrasting soybean cultivars. A total of 9,457 non-redundant, unambiguous, label-independent and repeatable phosphopeptides were subsequently identified from six experimental replicates, corresponding to 9,234 of deduced unique phosphoproteins. These soybean proteins contain a total of 20,880 phosphosites, 84.9% of which were found to be novel phosphosites of the soybean phosphoproteome. The overly post-translationally modified proteins is 2.05% of the phosphoproteins identified. Most of these extensively phosphorylated proteins are photoreceptors, mRNA-, histone- and phospholipid-binding as well as serine/threonine/tyrosine protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of the phosphosite of phosphoprotein follows the exponential decay law, Y=4.13e^(-0.098X)-0.04. From 218 significantly regulated unique phosphopeptide groups, 188 significantly regulated phosphoproteins were found, and they are enriched in biological functions of water transport and deprivation, methionine metabolic process, photosynthesis/light reaction, and response to cadmium ion, osmotic stress and ABA under drought treatment. A total of 15 and 20 drought-tolerant cultivar significantly regulated phosphoproteins are transcription factors and protein kinases/phosphatases, respectively. More than 50% of these phosphoproteins are considered to be novel regulatory components, presumably mediating the development of the soybean drought tolerance under water deprivation process. The association of five randomly selected phosphoproteins with the drought response was corroborated with the qRT-PCR method.
2021-09-09 | PXD022794 | Pride
Project description:The isotopic dimethyl labeling-based quantitative post-translational modification proteomics was applied to study the phosphoproteomic changes associated with the drought responses of two contrasting soybean cultivars. A total of 9,457 non-redundant, unambiguous, label-independent and repeatable phosphopeptides were subsequently identified from six experimental replicates, corresponding to 9,234 of deduced unique phosphoproteins. These soybean proteins contain a total of 20,880 phosphosites, 84.9% of which were found to be novel phosphosites of the soybean phosphoproteome. The overly post-translationally modified proteins is 2.05% of the phosphoproteins identified. Most of these extensively phosphorylated proteins are photoreceptors, mRNA-, histone- and phospholipid-binding as well as serine/threonine/tyrosine protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of the phosphosite of phosphoprotein follows the exponential decay law, Y=4.13e^(-0.098X)-0.04. From 218 significantly regulated unique phosphopeptide groups, 188 significantly regulated phosphoproteins were found, and they are enriched in biological functions of water transport and deprivation, methionine metabolic process, photosynthesis/light reaction, and response to cadmium ion, osmotic stress and ABA under drought treatment. A total of 15 and 20 drought-tolerant cultivar significantly regulated phosphoproteins are transcription factors and protein kinases/phosphatases, respectively. More than 50% of these phosphoproteins are considered to be novel regulatory components, presumably mediating the development of the soybean drought tolerance under water deprivation process. The association of five randomly selected phosphoproteins with the drought response was corroborated with the qRT-PCR method.
2023-05-10 | PXD022806 | Pride
Project description:A customized targeted oligoarray was used to monitor the expression levels of 1000 genes, representative of the immature kernel transcriptome. Using this oligoarray we compared transcripts from 10 DAP kernels of two susceptible and two drought tolerant genotypes. These four genotypes were extracted from our RIL population (B73xH99) and grown under water stress and well watered field conditions. Keywords: Stress response Two-condition experiment: water stress field condition vs. well watered field condition. Transcriptional profiling of 10 DAP kernel (two susceptible and two drought tolerant genotypes) in the first condition vs 10 DAP kernel (two susceptible and two drought tolerant genotypes) in the second condition. Hybridization replicates: 4 in dye swap mode. Two probes per gene per array.
2008-12-21 | E-GEOD-11568 | biostudies-arrayexpress
Project description:Two cultivars of Sorghum biocolor were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. Samples are from leaves and roots collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought. A liquid-based bottom up proteomics analysis was performed using an iTRAQ labeling multiplexing approach to determine relative abundances. After the peptides were digested with trypsin and iTRAQ labeled, they were fractionated into 12 fractions offline using a C-18 column under high-pH solvent conditions Each fraction was further separated on a low pH C-18 column with direct infusion into a ThermoScientific Q-Exactive mass spectrometer. See the supplementary files for iTRAQ reporter ions details.
2018-06-21 | MSV000082487 | MassIVE
Project description:Traditional rice varieties found in India have many desirable characteristics. Amongst them, their differential responses to abiotic and biotic stresses are of great agricultural importance. Drought or osmotic stress is one of the major abiotic stresses afflicting crop plants in India. Indigenous varieties like Dagad deshi have been found to be drought resistant and, thereby, are being studied in great detail by plant breeders and biotechnologists alike. In this study, we have analyzed the transcriptomes of two contrasting cultivars, i.e. Dagad deshi (tolerant) and IR20 (susceptible), under control and stress conditions to elucidate the differences in their responses to drought stress using Affymetrix microarray platform. Hydroponically grown seven-day-old seedlings of Dagad deshi and IR20 were subjected to drought stress by placing them on 3 mm Whatmann sheets under light for 3 h and 6 h at 28±1oC. For control samples, seedlings were kept in RGM (root growth medium) for 6 h at 28±1oC. RNA extracted from each sample was hybridized on rice Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. Overall, eighteen samples were analyzed representing control, 3 h and 6 h of dehydration stress for each cultivar (Dagad deshi and IR20).
2015-06-30 | E-GEOD-41647 | biostudies-arrayexpress