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:Salt Stress response of salt-tolerant genotype FL478 compared to IR29 Rice GeneChip was used to find differential expression between two rice genotypes under control and salt stress conditions Keywords: genotype and treatment comparison
2010-07-07 | GSE13735 | GEO
Project description:Salt Stress response of salt-tolerant genotype FL478 compared to IR29 Rice GeneChip was used to find differential expression between two rice genotypes under control and salt stress conditions Keywords: genotype and treatment comparison Roots (tips) tissue was used for hybridization to GeneChips
2010-07-07 | E-GEOD-13735 | biostudies-arrayexpress
Project description:Climate change is affecting crop production due to soil salinization and water scarcity, and is predicted to worsen in the coming years. Rice is a major staple food and the most salt-sensitive cereal. High salinity in the soil triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological, cellular and molecular levels. A major QTL for salinity tolerance, named Saltol, is present on chromosome 1 of Indian rice landrace varieties such as Pokkali and Nona Bokra. In this study, we characterized the physiological and early proteomic responses to salinity in FL478, an inbred rice line harboring the Saltol region. For this, plantlets were cultured in hydroponic cultures with 100 mM NaCl and evaluated at 6, 24 and 48h. At the physiological level, salinity significantly reduced shoot length after 48 h, whereas root length significantly increased. Moreover, the Na+/K+ ratio was maintained at lower levels in the shoots compared to the roots FL478 plantlets. On the other hand, roots showed a faster and more coordinated proteomic response than shoots, which was evident from only 6h of treatment. These responses were markedly related with transcription- and translation-related proteins. Moreover, roots exhibited a higher accumulation of stress-related proteins in response to salinity treatment, like peroxidase and SalT, which are both present in the Saltol QTL. Both, physiological and proteomic response, showed that roots respond in a highly adaptive manner to salinity stress compared to shoots, which suggests that this tissue is critical to the tolerance observed in varieties harbouring the Saltol region.
2020-12-21 | PXD014669 | Pride
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:Whole genome transcriptional responses is profiled in the 0 & 120 mM NaCl (salinity) stressed whole seedlings of the rice genotypes FL478, Hassawi, Nonabokra and IR29 using Agilent Rice Microarrays. 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). The transcriptomic data of these genotypes (submitted now) along with the previously submitted dataset (GSE79043) were used to develop traditional and orthogonal signal correction filtered partial least square discriminant analysis (OSC-PLSDA) models using the differential transcriptomic fingerprints in tolerant vs susceptible rice genotypes. These models are then used to test the transcriptomic fingerprints of stressed and unstressed samples of several genetically diverse rice genotypes in a way to predict their salinity tolerance status. The accuracy of the prediction using OSC-PLSDA model was higher compared to that of the traditional PLSDA model. Besides, the accuracy of the prediction of salinity tolerance of the salt stressed samples was higher than that of the unstressed samples indicating that the stress induced transcriptomic fingerprints can better discriminate the tolerance and susceptible genotypes.The minimum number of genes (109 genes) that highly contributed to the classification and model prediction of salinity tolerance status was identified using the Variable Importance vector in OSC-PLSDA model.This study provides an example of prediction model building using whole genome transcriptomic data. The fingerprints of such transcriptomic profiles could be used as possible markers for the overall prediction of tolerance or resistance to abiotic and biotic stresses, respectively.
2026-05-31 | GSE331250 | 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: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: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: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