Expression profiling of soybean genes in response to drought
Ontology highlight
ABSTRACT:
ORGANISM(S): Glycine max
SUBMITTER: Dung Le
PROVIDER: E-GEOD-40627 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Drought-responsive genes in soybean leaves were successfully identified using Affymetrix Soybean Gene 1.0 ST arrays on leaves samples of reproductive-stage soybean plants. R1 soybean plants planted in pots were imposed drought by withholding water for 5 days until the soil moisture content dropped to 5%, and 3rd trifoliates (now at the R2 stage) were collected for expression profiling. Soybean plants were grown in pots. When the plants reached the R1 stage (started flowering), drought treatment was imposed by withholding water. The soil moisture content was monitored during the process until the 5th day of water withholding, when soil moisture content reached 5%. The 3rd trifoliate (counting from shoots), now at the R2 stage, was collected for total RNA extraction, while other 3rd trifoliates of similar chlorophyl index were collected for leaves water content determination to identify the severity of the stress. Total RNA from 3rd trifoliates were used for expression profiling using Affymetrix Soybean Gene 1.0 ST arrays. Four biological repeats per treatment were performed, three biological repeats were chosen for expression profiling.
2012-11-10 | E-GEOD-40604 | biostudies-arrayexpress
Project description:Drought-responsive genes in soybean leaves were successfully obtained using soybean gene 1.0 ST array. Leaf samples from the vegetative stage of soybean plants were used. V6 soybean plants planted in the pots were imposed drought by withholding water for 6 days until the soil moisture content drop to 5% and trifolium 4th were collected for expression profiling
2012-04-02 | E-GEOD-29663 | biostudies-arrayexpress
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:Soybean (Glycine max) is susceptible to root rot when subjected to continuous cropping, and this disease can seriously diminish the crop yield. Herein, isobaric tag for relative and absolute quantitation (iTRAQ) labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were employed for proteomic analysis of continuously cropped soybean inoculated with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae. Differential expression of proteins in soybean roots was determined following 1 year of continuous cropping. A total of 131 differentially expressed proteins (DEPs) were identified in F. mosseae-treated samples, of which 49 and 82 were up- and down-regulated, respectively. The DEPs were annotated with 117 Gene Ontology (GO) terms, with 48 involved in biological processes, 31 linked to molecular functions, and 39 associated with cell components. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis mapped the DEPs to 113 mainly metabolic pathways including oxidative phosphorylation, glycolysis and amino acid metabolism. Expression of glucan 1,3-beta-glucosidase, chalcone isomerase, calcium-dependent phospholipid binding and other defense-related proteins was up-regulated by F. mosseae, suggesting inoculation promotes the growth and development of soybean and increases disease resistance. The findings provide an experimental basis for further research on the molecular mechanisms of AM fungi in resolving problems associated with continuous soybean cropping.
2019-11-12 | PXD009911 | Pride
Project description:Rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. However, the underlying mechanisms are unclear. Here, we investigated the responses to ozone of two rice (Oryza Sativa L.) cultivars, Sasanishiki and Habataki. Sasanishiki showed ozone-induced leaf injury, but no grain yield loss. By contrast, Habataki showed grain yield loss with minimal leaf injury. A QTL associated with grain yield loss caused by ozone was identified in Sasanishiki/Habataki chromosome segment substitution lines and included the ABERRANT PANICLE ORGANIZATION 1 (APO1) gene. The Habataki allele of the APO1 locus in a near-isogenic line also resulted in grain yield loss upon ozone exposure, suggesting APO1 involvement in ozone-induced yield loss. Only a few differences in the APO1 amino acid sequences were detected between the cultivars, but the APO1 transcript level was oppositely regulated by ozone exposure: i.e., it increased in Sasanishiki and decreased in Habataki. Interestingly, the levels of some phytohormones (jasmonic acid, jasmonoyl-L-isoleucine, and abscisic acid) known to be involved in attenuation of ozone-induced leaf injury tended to decrease in Sasanishiki but to increase in Habataki upon ozone exposure. These data indicate that ozone-induced grain yield loss in Habataki is caused by a reduction in the APO1 transcript level through an increase in the levels of phytohormones that reduce leaf damage. Ozone induced gene expression in rice inflorescence meristem was measured at 6 month after exposure to dose of 43.7 nL L-1 (ambient air) and 85.7 nL L-1 (2-fold concentration compared to ambient air) (12 hours mean). The two culticars, Sasanishiki and Habataki, were used for each experiment.
2015-01-31 | E-GEOD-65465 | biostudies-arrayexpress
Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.
2020-01-22 | PXD000319 | Pride
Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level. Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers VM-CM-6tsch VB 1514 (VM-CM-6tch Industrietechnik GmbH, Germany) with a 16/8 h (light/dark) photoperiod at 22/18 M-BM-0C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity. The Pseudomonas syringae pv. tomato strain DC3000 culture was grown overnight in 10 ml of Kings B solution supplemented with antibiotics rifampicin (50 M-NM-<g mlM-bM-^HM-^R1) and kanamycin (25 M-NM-<g mlM-bM-^HM-^R1). Overnight culture was washed once in 10 mM MgCl2 and final cell densities were adjusted to approximately 0.20 at 600 nm (approximately 1.5 M-CM-^W 108 cfu mlM-bM-^HM-^R1) in 10 mM MgCl2. Plants were mock-challenged with 10 mM MgCl2 or inoculated with DC3000 strain, 3-4 leaves were infiltrated on the abaxial surface with a needleless 1-ml syringe.Whole rosettes were cut at the hypocotyls and harvested from Pseudomonas infested and mock-infected plants after 72 hours treatment. 4 biological replicates were prepared from each treatment, each containing rosettes from 15 individual plants. Differences in transcriptional responses were measured by comparing genes expression of Pseudomonas infected plants against mock-infected control plants.
2013-06-01 | E-GEOD-39246 | biostudies-arrayexpress
Project description:To investigate the response of poplar hybrids to drought, leaves were collected from plants to which water was suspended for 8 and 13 days. After measuring the respective relative water content, RNAs were isolated from leaves of moderately and severely droughted plants and from control plants, and Illumina RNA sequencing was performed to analyze RNA synthesis in these tissues. Transcriptional profiling of leaves of poplar plants subjected to 8 or 13 days of water deprivation. Sequence data were generated by deep sequencing, on four replicates (2 per 2 hybrids), using Illumina HiSeq2000.
2015-01-21 | E-GEOD-64044 | biostudies-arrayexpress
Project description:Environmental stresses such as drought, salinity and both high and low temperature are frequently faced by crops all over the world and can be considered major limiting factors for plant geographical distribution and productivity. Breeding has allowed creation of crops more adapted to some of the adverse environmental conditions and to overcome the geographical limitation without major consequences to productivity. However, due to the climate changes observed in the last few decades, some agricultural areas have experienced the âgreen seed problemâ characterized by chlorophyll retention in mature seeds. This is problematic in oil seed crops such as soybean and canola since it is related to lower seed and oil quality, resulting in serious financial losses. Besides the environmental factors, there are also genetic components controlling the susceptibility of different cultivars to green seed production. Understanding the molecular mechanisms controlling chlorophyll retention in seeds is crucial to allow advanced molecular breeding techniques and genetic engineering as a way to increase tolerance to this growing problem. We have used maturing soybean seeds of the cultivar MG/BR 46, harvested in R6, R7 and R8, produced under non-stressed and stressed environmental conditions, to understand he molecular basis of chlorophyll degradation and, consequently, its retention during soybean seed maturation. Soybean seeds were produced under stressed and non-stressed conditions and harvested in 3 different stages of maturation: R6 non-stressed, R7 non-stressed, R8 non-stressed, R6 stressed, R7 stressed, R8 stressed.
2016-01-21 | E-GEOD-70999 | biostudies-arrayexpress
Project description:Competition is a major determinant of plant community structure consisting of both species-specific and general interactions, either of which may influence competitive competency and plant abundance and size. In certain cases, competitive competency could arise from altered gene expression and plant function when an individual is confronted with new competitors. We explored competition at the molecular level by hybridizing transcripts from Centaurea maculosa (spotted knapweed), one of North America's most invasive exotic plant species, to an Arabidopsis microarray chip. Centaurea was grown in competition with Festuca idahoensis (Idaho fescue), a native grass species that generally has weak competitive effects against Centaurea; Gaillardia aristata (Indian blanketflower), a native herbaceous species that tends to be a much stronger competitor against Centaurea; or alone (control). The expression of some genes was found to be relatively uninfluenced by the type of plant neighbor, whereas other patterns of gene expression appeared to be more neighbor specific. To our knowledge, these results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbors and provide a new avenue of insight into the molecular aspects of plant competitive ability. Keywords: treated vs.untreated Files; chip 618 (12-7-05) and chip 623 (1-20-06) are replicates. One channel is root cDNA from Centaurea maculosa grown in isolation and the other channel is root cDNA from Centaurea maculosa grown with a strong competitor, Gaillardia aristata. For each chip, RNA extractions on unique biological samples were performed. Files; chip 720 (2-23-06) and chip 723 (3-17-06) are replicates. One channel is root cDNA from Centaurea maculosa grown in isolation and the other channel is root cDNA from Centaurea maculosa grown with a weak competitor, Festuca idahoensis. For each chip, RNA extractions on unique biological samples were performed.
2010-05-17 | E-GEOD-7444 | biostudies-arrayexpress