Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1012700 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25897900_1.fastq.gz | Fastqsanger.gz | |||
| SRR25897900_2.fastq.gz | Fastqsanger.gz | |||
| SRR25897901_1.fastq.gz | Fastqsanger.gz | |||
| SRR25897901_2.fastq.gz | Fastqsanger.gz | |||
| SRR25897902_1.fastq.gz | Fastqsanger.gz |
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Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance. In this study, the gene expression patterns across two organs including leaves and roots at seedling stage were characterized under control, salinity, salinity+ABA treatments by using the Affymetrix rice microarray platform based on a salinity tolerant rice line derived from IR64.
2015-11-02 | E-GEOD-58603 | biostudies-arrayexpress
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance.
2015-11-02 | GSE58603 | GEO
Project description:Melatonin plays a potential role in multiple plant developmental processes and stress response. However, there are no reports regarding exogenous melatonin promoting rice seed germination under salinity and nor about the underlying molecular mechanisms at genome-wide. Here, we revealed that exogenous application of melatonin conferred roles in promoting rice seed germination under salinity. The putative molecular mechanisms of exogenous melatonin in promoting rice seed germination under high salinity were further investigated through metabolomic and transcriptomic analyses. The results state clearly that the phytohormone contents were reprogrammed, the activities of SOD, CAT, POD were enhanced, and the total antioxidant capacity was activated under salinity by exogenous melatonin. Additionally, melatonin-pre-treated seeds exhibited higher concentrations of glycosides than non-treated seeds under salinity. Furthermore, exogenous melatonin alleviated the accumulation of fatty acids induced by salinity. Genome-wide transcriptomic profiling identified 7160 transcripts that were differentially expressed in NaCl, MT100 and control. Pathway and GO term enrichment analysis revealed that genes involved in the response to oxidative stress, hormone metabolism, heme building, mitochondrion, tricarboxylic acid transformation were altered after melatonin pre-treatment under salinity. This study provides the first evidence of the protective roles of exogenous melatonin in increasing rice seed germination under salt stress, mainly via activation of antioxidants and modulation of metabolic homeostasis.
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Project description:44K oligo microarray analysis was performed for monitoring salinity stress–inducible genes in rice.
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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.
2021-06-15 | E-MTAB-10653 | biostudies-arrayexpress
Project description:Rice (Oryza sativa) stands among the world's most important crop species and is salt-sensitive. The undue accumulation of sodium ions (Na+) in shoots has the strongest negative correlation with rice productivity under long-term salinity. The plasma membrane Na+/H+ exchanger protein SOS1 is the only Na+ efflux transporter that has to date been genetically characterized and only in dicot plants. Here, the importance of Na+ fluxes governed by the SOS system in the salt tolerance of rice was analyzed by a reverse-genetics approach. A sos1 loss-of-function mutant displayed exceptional salt sensitivity that correlated with excessive Na+ intake and impaired Na+ loading into the xylem. Thus, SOS1 controls net Na+ uptake by roots and the long-distance transport to shoots. The acute Na+ sensitivity of sos1 plants at low NaCl concentrations allowed the inspection of the transcriptional response to sodicity stress, without interference by the osmotic challenge intrinsic to high salinity treatments. The transcriptional response to salt of the sos1 mutant roots involved the preferential down-regulation of stress-related genes compared to the wild-type despite the greater intensity of the stress imposed to the mutant, which suggested impaired stress detection or inability to mount a comprehensive response to salinity.
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Project description:Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates. Keywords: Comparison of gene expression in three tissues with stress treatment and without treatment To globally elucidate potential genes involved in drought and high-salinity stresses responses in rice, an oligomer microarray covering 37,132 genes including cDNA or EST supported and putative genes was applied to study the expression profiling of shoot, flag leaf, and panicle under drought or high-salinity treatment. Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates.
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Project description:We designed an array based on the release 7 of Michigan State University (MSU) rice genome annotation database (http://rice.plantbiology.msu.edu). The array was used for investigating the expression divergence and regulation between two contrasting rice genotypes under high salinity stress.
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Project description:RSS1 is required for maintenance of meristematic activity under salinity conditions in rice. We carried out transcriptome analysis using shoot basal tissues in wild type and rss1-2 grown under non-stress and salt-stress conditions.
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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.
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