Transcriptome profiling from roots of jatropha in response to waterlogging
Ontology highlight
ABSTRACT:
ORGANISM(S): Jatropha curcas
SUBMITTER: Piyada Juntawong
PROVIDER: E-GEOD-57428 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response Plants of cotton cultivar Sicot 71 were grown to the two-leaf stage in tubs. For stress treatments plants were either watered as normal or flooded with water to completely submerge the root system. At four and twenty-four hours post-flooding samples of root or leaf tissue were taken from control and flooded plants. Total RNA was extracted from each tissue sample and assayed on cotton Affymetrix chips. Two biological replications were used for each comparison.
2010-05-17 | E-GEOD-16467 | biostudies-arrayexpress
Project description:Waterlogging of plants leads to low oxygen levels (hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and protein synthesis. Our research seeks to characterize the gene regulatory networks associated with short-term waterlogging. MicroRNAs (miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic responses. To characterize the involvement of miRNAs in response to hypoxia conditions, a quantitative reverse transcriptase PCR (qRT-PCR) assay was used to profile the expression changes of the 22 candidate mature miRNAs, which were selected from small RNA library of waterlogging resistant line Hz32 and 84 of their predicted targets in three inbred Zea mays lines that showed different tolerance to waterlogging. Based on our studies, miR164, miR167, miR172, miR408 and miR528, which are involved in aerenchyma and root cap formation, lateral root development, root/shoot elongation and plant cell detoxification, found to be key regulator under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress-related cis-regulatory elements on the promoters of these miRNAs using the B73 reference and a miRNA-mediated gene regulatory network was constructed. The differential expression patterns of miRNAs and their targets in these three inbred lines suggest that the miRNAs are active participants in the signal transduction at the early stage of hypoxia conditions via a complex network and biochemical pathways. Our study also suggests that there might be a miRNA-mediated energy-saving strategy in surviving from waterlogging. Examination of miRNA expression in maize root under 4h waterlogging treatment
2011-10-15 | E-GEOD-32983 | biostudies-arrayexpress
Project description:Gene expression analysis by high-throughtput RNA-sequencing from roots of waterlogged jatropha (Jatropha curcas). Six leaf stage seedlings (~30 d.o.) were subjected to 24 h of soil waterlogging.
2014-11-05 | GSE57428 | GEO
Project description:To adapt to waterlogging in soil, some gramineous plants, such as maize (Zea mays), form lysigenous aerenchyma in the root cortex. Ethylene, which is accumulated during waterlogging, promotes aerenchyma formation. Aerencyma is formedonly in cortex in maise root. Therevore, aerenchyma is one of the model of programmed cell death. However, the molecular mechanism of aerenchyma formation is not understood. Therefore we isolated only cortex cells in maize primary root using laser microdissection. And microarray analysis was perforemed to identify the arechyma formation related genes. For microarray analysis, we designed 4 different experiments. Basal part and apical part of root were used for 1st experiment because arenchyma was formed in basal part of root, but not in apex. In second experiment, basal part of root with 6 hours waterlogged treatment and without treatment were used. And, as aerenchyma was induced by ethylene, ethylene and 1-MCP (inhibitor of ethylen perception) were used for experiment3 and 4. Gene expression analysis in 4 kinds of samples (cortex in basal reagion of maize primary root which were treated with waterlogged condition, aerobic condition, ethylene and 1-MCP and cortex in apical reagion of maize primary root which were treated with waterlogged conditio)
2011-01-28 | E-GEOD-26897 | biostudies-arrayexpress
Project description:Aerenchyma is a specialized tissue consisting of longitudinal gas spaces, which enables internal movement of gases (e.g., O2, CO2, ethylene and methane), in plant roots, petioles and stems. Especially, internal transport of oxygen via aerenchyma from shoots to roots is very important for adaptation or survival of plants under waterlogged condition. To identify aerenchyma formation-associated genes expressed in maize root, we used LM combined with a microarray for monitoring genes expressed in root cortical cells under three conditions: under aerobic condition and under waterlogged condition with and without pretreatment with 1-MCP, an inhibitor of ethylene perception. For the waterlogging treatments, the primary root (but not the shoots) was waterlogged. Two and half day-old-seedlings were pre-treated with an inhibitor of ethylene perception 1-methylcyclopropene (1-MCP; 1 ppm) for 12 hours before the waterlogging treatment. Three-day-old seedlings were growing under aerated condition at the same time with other treatments as a control. Total RNA was extracted from root cortex cells from the segment of the primary root, 0.5 cm long: from 1.5 to 2 cm from the junction shoot-root derived from 3-days-old maize seedlings, and subjected to 44k oligo-DNA microarray (1. Aerated vs Hypoxia, 2. Hypoxia+MCP vs Hypoxia) with 3 biological replicates and color swaps.
2010-07-31 | E-GEOD-22943 | biostudies-arrayexpress
Project description:Genome-wide transcriptome analysis was performed to understand the expression pattern of transcriptomes in tolerant and susceptible subtropical maize genotypes under waterlogging stress condition. Waterlogging stress causes yield reduction in maize (Zea mays). It is important to dissect the genetic circuits that underlie the plant responses to waterlogging. So, the experiment was designed with the following objectives: to understand the expression pattern of transcriptomes in the tolerant and the susceptible genotypes under waterlogging stress; to identify DEGs functioning in important pathways underlying adaptive traits; to co-map bin locations of the transcriptomes with already known QTLs for waterlogging and find synteny with other species; and to generate gene co-expression networks to study cohorts of genes expressed together in modules and functional cluster, while comparing the two genotypes. Two tropical maize (Zea mays L.) inbred lines, HKI1105 (tolerant) and V-372 (susceptible), were used for our experiment. The genotypes were sown in plastic pots filled with loam soil with sandy texture. The plants were watered daily to soil capacity until the application of stress at 28 days after sowing. To impose waterlogging condition, the perforation in the bottom of the pots (35 cm in height) was sealed and the stress treatment was given by watering the pots (5 cm standing water) for seven continuous days. To allow for recovery from stress, the perforations of the pots were unsealed for proper drainage of excess water. The root samples from both genotypes were collected on the 28th, 32nd, 35th and 42nd day after sowing, which represented control, moderate stress, severe stress and post-stress recovery stages, respectively. Two biological replications were used for each comparison.
2013-08-14 | E-GEOD-43088 | biostudies-arrayexpress
Project description:Soil waterlogging is one of the major abiotic stresses affecting maize growth and yields. To understand the molecular mechanisms underlying waterlogging tolerance in maize, the iTRAQ LC-MS/MS technique was employed to map the proteome of seedling root cells of the A3237 (tolerant inbred) and A3239 (sensitive inbred) lines under control and waterlogged conditions. Among the 3373 identified proteins, 293 were differentially abundant proteins (DAPs), of which 207 originated in A3237 and 158 in A3239. These DAPs were categorized into 11 groups that are closely related to plant defence responses, including metabolism, energy, disease/defense and transport. In the tolerant line A3237, NADP-malic enzyme, glutamate decarboxylase, coproporphyrinogen III oxidase, glutathione S-transferase TAU 25, glutathione dehydrogenase and xyloglucan endotransglycosylase 6 were specifically accumulated to manage energy, maintain pH levels and minimize oxidative damage in waterlogged root cells.
2014-11-18 | PXD001125 | Pride
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response
2009-12-18 | GSE16467 | GEO
Project description:Abstract Background: Exogenous 6-benzyladenine (6-BA) could improve leaf defense system activity. In order to better understand the regulation mechanism of exogenous 6-benzyladenine (6-BA) on waterlogged summer maize, three treatments including control (CK), waterlogging at the third leaf stage for 6 days (V3-6), and application of 100 mg dm-3 6-BA after waterlogging for 6 days (V3-6-B), were employed using summer maize hybrid DengHai 605 (DH605) as the experimental material. We used a labeling liquid chromatography-based quantitative proteomics approach with tandem mass tags to determine the changes in leaf protein abundance level at the tasseling stage. Results: Waterlogging significantly hindered plant growth and decreased the activities of SOD, POD and CAT. In addition, the activity of LOX was significantly increased after waterlogging. As a result, the content of MDA and H2O2 was significantly increased which incurred serious damages on cell membrane and cellular metabolism of summer maize. And, the leaf emergence rate, plant height and grain yield were significantly decreased by waterlogging. However, application of 6-BA effectively mitigated these adverse effects induced by waterlogging. Compared with V3-6, SOD, POD and CAT activity of V3-6-B were increased by 6.9%, 12.4%, and 18.5%, LOX were decreased by 13.6%. As a consequence, the contents of MDA and H2O2 in V3-6-B were decreased by 22.1% and 17.2%, respectively, compared to that of V3-6. In addition, the leaf emergence rate, plant height and grain yield were significantly increased by application of 6-BA. Based on proteomics profiling, the proteins involved in protein metabolism, ROS scavenging and fatty acid metabolism were significantly regulated by 6-BA, which suggested that application of 6-BA exaggerated the defensive response of summer maize at proteomic level. Conclusions: These results demonstrated that 6-BA had contrastive effects on waterlogged maize. By regulating key proteins related to ROS scavenging and fatty acid metabolism, 6-BA effectively increased the defense system activity of waterlogged summer maize, then balanced the protein metabolism and improved the plant physiological traits and grain yield.
2020-05-27 | PXD016743 | Pride
Project description:To better understand the molecular mechanisms of the response of S. cannabina to soil waterlogging, the transcriptional profile in both short and long term of waterlogged S. cannabina roots were performed using the Illumina HiSeq™ 2000 sequencing platform (Illumina Inc., San Diego, CA, USA). Bioinformatic analysis of transcriptome data was performed to allow identification and functional annotation of differentially expressed genes (DEGs). By comparing the different genes appeared in control and treatment groups, we can learn more about the species-specific responses employed by S. cannabina and find novel associated genes or strategies in waterlogging resistant species.
2017-09-20 | GSE92670 | GEO