Root-specific transcriptional profiling of contrasting rice genotypes in response to salinity stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Indica Group
PROVIDER: GSE14403 | GEO | 2009/07/16
SECONDARY ACCESSION(S): PRJNA111791
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice. Experiment Overall Design: Seedlings were cultured in sand and irrigated with a nutrient solution for 22 d (salt-treated) and 30 d (control) after germination, respectively. Salinity treatment was applied by adding NaCl and CaCl2 (5:1 molar concentration) in two steps over a period of 3 days (final electrical conductivity: 7.4 dS m-1) to prevent osmotic shock. All plants were harvested on day 30.
2009-08-07 | E-GEOD-14403 | biostudies-arrayexpress
Project description:Whole genome transcriptional responses is profiled in the 0 & 120 mM NaCl stressed whole seedlings of four indica (Pokkali, PSBRc50, IR 58, BRRI dhan 29), two Japonica (Banikat, Nipponbare) and two wild (O. latifolia, O. Rufipogon) accessions of rice (that showed varied level of tolerance to salt stresses) to identify the salinity induced transcripts. Stress was imposed on 14 day old seedlings and total RNA from the whole seedlings was collected after 48 h of stressed period (i.e., from 16 day old seedlings). These data sets were used for two different analyses. Firstly, the gene expression responses of eight rice genotypes was interrogated by the weighted continuous morpho-physiological trait responses (on a scale of 0 to 1) using a modified version of the ‘Significance Analysis of Microarrays’ (SAM) to identify the genes whose expression changes significantly and which is relative to the changes in morpho-physiological traits over these rice genotypes. Secondly, the differentially expressed significant salinity induced genes were also identified in the tolerant and in the susceptible genotypes using Gene-spring software. The genes that enriched the important biological processes and molecular functions (as identified by Gene Ontology: Singular enrichment analysis) are discussed in a way to explain the roles of these genes in overall stress adaptation mechanism.
2016-03-10 | GSE79043 | GEO
Project description:Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Experiment Overall Design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).
2008-11-05 | E-GEOD-4438 | biostudies-arrayexpress
Project description:Whole genome transcriptional responses is profiled in the 0 & 120 mM NaCl stressed whole seedlings of four indica (Pokkali, PSBRc50, IR 58, BRRI dhan 29), two Japonica (Banikat, Nipponbare) and two wild (O. latifolia, O. Rufipogon) accessions of rice (that showed varied level of tolerance to salt stresses) to identify the salinity induced transcripts. Stress was imposed on 14 day old seedlings and total RNA from the whole seedlings was collected after 48 h of stressed period (i.e., from 16 day old seedlings). These data sets were used for two different analyses. Firstly, the gene expression responses of eight rice genotypes was interrogated by the weighted continuous morpho-physiological trait responses (on a scale of 0 to 1) using a modified version of the â??Significance Analysis of Microarraysâ?? (SAM) to identify the genes whose expression changes significantly and which is relative to the changes in morpho-physiological traits over these rice genotypes. Secondly, the differentially expressed significant salinity induced genes were also identified in the tolerant and in the susceptible genotypes using Gene-spring software. The genes that enriched the important biological processes and molecular functions (as identified by Gene Ontology: Singular enrichment analysis) are discussed in a way to explain the roles of these genes in overall stress adaptation mechanism. Fourteen day old whole seedlings of 8 rice genotypes were treated with 0 & 120 mM NaCl stress for 48 hours each with three replications and the gene expressions were measured using Agilent Rice Gene Expression 4x44K Microarray.
2016-03-10 | E-GEOD-79043 | biostudies-arrayexpress
Project description:Over the years, many traditional rice varietites of India were sourced and studied owing to their ability to withstand abiotic pressures like excessive salinity in the soil and water. These cultivars growing in specific areas of the country represent a rich gene pool from where a deeper understanding of the processes underlying tolerance to abiotic stress can be gained. Indigenous varieties like Nonabokra and Pokkali are known salt tolerant varieties and are being studied in great detail. In the present study, we have analyzed the transcriptomes of the contrasting cultivars; Nonabokra (tolerant), Pokkali (tolerant) and IR29 (susceptible) in order to decipher the differences in their responses to salinity stress by utilizing microarray.
2021-12-31 | GSE41650 | GEO
Project description:Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. Therefore, simultaneous comparison of transcriptional and translational changes between IR29 and Pok could unravel molecular insights into gene regulatory mechanisms that differ between these contrasting genotypes. Using RNA-Seq, we analyzed transcriptome and translatome from the control and salt-exposed Pok and IR29 seedlings. Clear differences were evident both at transcriptional and translational levels between the two genotypes even under control condition. In response to salt stress, 57 DEGs were commonly upregulated both at transcriptional and translational levels in the two genotypes; the number of up/down regulated DEGs in IR29 was comparable at transcriptional and translational levels; whereas in Pok, the number of upregulated DEGs at translational level (544 DEGs) was considerably higher than that at transcriptional level (219 DEGs); contrastingly, the number of downregulated DEGs (58) at translational level was significantly smaller than that at transcriptional level (397 DEGs). We speculate that Pok is more capable of stabilizing mRNA as well as can efficiently load mRNAs on to polysomes for translation under salt stress. Functional analysis showed that Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis under salt stress. The present study not only confirmed the known salt stress associated genes, but also identified a number of putative new salt-responsive genes. This study also showed the importance of translational regulation in salt stress and other stresses responsive mechanism.
2019-01-15 | GSE119721 | GEO
Project description:Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. Therefore, simultaneous comparison of transcriptional and translational changes between IR29 and Pok could unravel molecular insights into gene regulatory mechanisms that differ between these contrasting genotypes. Using RNA-Seq, we analyzed transcriptome and translatome from the control and salt-exposed Pok and IR29 seedlings. Clear differences were evident both at transcriptional and translational levels between the two genotypes even under control condition. In response to salt stress, 57 DEGs were commonly upregulated both at transcriptional and translational levels in the two genotypes; the number of up/down regulated DEGs in IR29 was comparable at transcriptional and translational levels; whereas in Pok, the number of upregulated DEGs at translational level (544 DEGs) was considerably higher than that at transcriptional level (219 DEGs); contrastingly, the number of downregulated DEGs (58) at translational level was significantly smaller than that at transcriptional level (397 DEGs). We speculate that Pok is more capable of stabilizing mRNA as well as can efficiently load mRNAs on to polysomes for translation under salt stress. Functional analysis showed that Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis under salt stress. The present study not only confirmed the known salt stress associated genes, but also identified a number of putative new salt-responsive genes. This study also showed the importance of translational regulation in salt stress and other stresses responsive mechanism.
2019-01-15 | GSE119720 | GEO
Project description:Rice (Oryza sativa), the major staple food crop is being cultivated under varying ecosystems ranging from irrigated lowland to rainfed upland environments. Improvement in the rice production under drought prone unfavourable environment depends on the development of drought tolerant genotypes which needs thorough understanding of physiological and molecular events behind the tolerance mechanism. There is considerable genetic variation for drought tolerance mechanism within the cultivated gene pool. To understand the diversity of drought response, two indica rice genotypes namely, i) Apo, an up-land drought tolerant indica veriety from Philippines and ii) IR64, a popular high yielding drought susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under control and drought stressed conditions during vegetative phase. Keywords: Drought response
2012-05-01 | GSE5978 | GEO
Project description:Since metabolites are the net products of the central dogma of cellular biology, this study was aimed to decipher salinity tolerance depends on the information encoded by the metabolomic profiles of the salt tolerant ‘Umsila’ and susceptible ‘Zabad’ cultivars when grown under salinity. Changes in the metabolomic profiles of the leaf and root tissues were determined using hydrophilic interaction liquid chromatography (HILIC) and reverse phase liquid (RPLC) mass spectrometry.
2019-03-18 | ST001156 | MetabolomicsWorkbench
Project description:Rice (Oryza sativa), the major staple food crop is being cultivated under varying ecosystems ranging from irrigated lowland to rainfed upland environments. Improvement in the rice production under drought prone unfavourable environment depends on the development of drought tolerant genotypes which needs thorough understanding of physiological and molecular events behind the tolerance mechanism. There is considerable genetic variation for drought tolerance mechanism within the cultivated gene pool. To understand the diversity of drought response, two indica rice genotypes namely, i) Apo, an up-land drought tolerant indica veriety from Philippines and ii) IR64, a popular high yielding drought susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under control and drought stressed conditions during vegetative phase. Keywords: Drought response We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during drought stress. We used two contrasting rice genotypes (IR64 drought susceptible and Apo drought tolerant) differing in their degree of drought tolerance. Plants were grown under green house conditions and drought stress was imposed on 33rd DAS. Leaf sampling was done in both control and drought stressed plants after 6 days of drought stress. Three replications of microarray experiments were carried out by hybridizing the control samples against the drought stressed samples.
2012-04-30 | E-GEOD-5978 | biostudies-arrayexpress