Developing miRNA profiles for decoding salt stress tolerance in Pokkali rice
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ABSTRACT:
PROVIDER: PRJNA438114 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6829480.fastq.gz | Fastqsanger.gz | |||
| SRR6829481.fastq.gz | Fastqsanger.gz | |||
| SRR6829482.fastq.gz | Fastqsanger.gz | |||
| SRR6829483.fastq.gz | Fastqsanger.gz |
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Project description:We report the application of small RNA sequencing (Illumina) technology for the identification of miRNA from root and leaf tissues of pokkali rice cultivar grown under normal and salt stress conditions. We used this data to predict and identify known and novel miRNAs.
2021-02-01 | GSE111767 | GEO
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. Keywords: stress response
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Project description:Oryza sativa Indica group Pokkali (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 4 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.
2020-01-01 | E-MTAB-1914 | biostudies-arrayexpress
Project description:We initiated the project to identify new QTL regulating the salt tolerance in rice. We carried out linkage mapping using 148 recombinant inbred lines derived from IR29 and Pokkali. The extracted genomic DNA was subjected to genotyping with single-nucleotide polymorphism (SNP) markers using an Affymetrix Axiom Rice 56k SNP Genotyping Array.The manuscript related to the project is "Identification of new QTL for salt tolerance from rice variety Pokkali".
2019-05-31 | PRJEB32735 | EVA
Project description:The advent of next generation sequencing (NGS) has greatly enriched the database of miRNAs. For plants so far 8455 miRNAs sequences from 73 species and 15401 miRNAs sequences from 150 species have been deposited in miRBase 21.0 and Plant Non-coding RNA Database, respectively. The occurrence of miRNAs in such a huge number, which is still increasing, is because of the fact that the profile of miRNAs expression differs greatly from species to species, both quantitatively and qualitatively. Besides, even within a species it is expected that the miRNA expression profile would differ from cultivar to cultivar depending on the trait with regard to which the two cultivars differ, and on the same logic it is also expected that their expression profile would differ considerably in the plant under contrasting environmental conditions. However, report on comparative study of expression profile of miRNAs in rice cultivars, or in any crop cultivars, contrast for salt tolerance, or tolerance to any abiotic stress is scant. Therefore, the current study was planned to see the expression profile of miRNAs in a salt-tolerant rice (Oryza sativa L. ssp indica) cultivar (cv.) Pokkali in presence and absence of NaCl and to check the response pattern of a few important salt-responsive miRNAs in a salt-sensitive rice cultivar Badami in order to identify the miRNAs and their targets that could be involved in the salt tolerance process
2019-07-06 | GSE133866 | 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: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: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.
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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.
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