Gene expression profiling of Bruguiera gymnorhiza under salt stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Bruguiera gymnorhiza
PROVIDER: GSE10942 | GEO | 2008/05/01
SECONDARY ACCESSION(S): PRJNA107257
REPOSITORIES: GEO
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Project description:To identify key genes in the regulation of salt tolerance in the mangrove plant Bruguiera gymnorhiza, the transcriptome profiling under salt stress was carried out. Main roots and lateral roots were collected from the mangrove plants at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment. Samples were collected from each set of three trees at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment, that is 27 trees were used in total. RNA was extracted from mixture of the samples from 3 trees to average genotypes of 3 trees.
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Project description:Increasing soil salinization has led to severe losses of plant yield and quality. Researching the formation of plant salt tolerance and the molecular mechanism of the salt stress response is therefore urgent. We here take advantage of recent progress in single-cell transcriptomics technology to systematically analyze plant roots response to salt stress, and 57,185 high-quality cells were totally obtained from 5-day-old lateral root tips of Gossypium arboreum under natural growth and different salt-treatment conditions. Eleven cell types with an array of novel marker genes were identified and confirmed with RNA in situ hybridization. Pseudotime analysis on epidermal and root hair cells indicated the differentiation trajectory, and differential root-type cells responding to salt stress resulted in more epidermal and less endodermal cells. Abundant differentially expressed genes (DEGs) were found to be engaged in glycometabolism, reactive oxygen species hemeostasis, and phosphatidylinositol and MAKP signal pathways through functional enrichment analyses. Some candidate DEGs related with transcription factors and plant hormones responding to salt stress were also screened, which requires further functional verification to reveal the regulatory model of the plant roots response to salt stress. Combined with bulk RNA-seq data, a common DEG (Ga08G2497) annotated as Aldo-keto reductase-1 (AKR1) was selected to perform virus-induced gene silencing verification, and the silencing of GaAKR1 gene in G. arboreum resulted in severe stress-susceptibility phenotype, shorter root length, and less number of lateral roots. Physiological and biochemical detection also demonstrated that GaAKR1-silenced plants suffered more serious oxidative damages and, indicating that GaAKR1 might participates in salt tolerance of cotton by oxidation-reduction process. For the first time, we characterized a transcriptional atlas of plant roots under salt stress at a single-cell resolution, which explored the cellular heterogeneity, differential root-type cells, and differentiation trajectory, while providing valuable insights into the molecular mechanism underlying stress tolerance in plants.
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Project description:Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments. A reference design was used to analyze gene expression differences. Salt stressed young roots were harvested from seedlings of C. tagal at the ends of each shock duration. Young roots of unshocked seedlings were used as controls and harvested at the same time. Three biological replicates were set up for each treatment and corresponding control, respectively, each containing a pool of total RNA from 4 seedlings. Salt stressed samples were compared with the corresponding controls at each time point by co-hybridizing to the customized cDNA arrays
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Project description:Isoprene, a volatile hydrocarbon, is typically emitted from the leaves and other aboveground plant organs; isoprene emission from roots is not well studied. Given its well-known function in plant growth and defense aboveground, isoprene may also be involved in shaping root physiology to resist belowground stress. We used isoprene-emitting transgenic lines (IE) and a non-emitting empty vector and/or wild type lines (NE) of Arabidopsis to elucidate the roles of isoprene in root physiology and salt stress resistance. We assessed root phenotype and metabolic changes, hormone biosynthesis and signaling, and stress-responses under normal and saline conditions of IE and NE lines. We also analyzed the root transcriptome in the presence or absence of salt stress. IE lines emitted isoprene from roots, which was associated with higher primary root growth, root biomass, and root/shoot biomass ratio under both control and salt stress conditions. Transcriptome data indicated that isoprene altered the expression of key genes involved in hormone metabolism and plant responses to stress factors. Our findings reveal that root constitutive isoprene emission sustains root growth also under salinity by regulating and/or priming hormone biosynthesis and signaling mechanisms, amino acids biosynthesis, and expression of key genes relevant to salt stress defense.
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Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.
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