Salt stress study on different rice varieties
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ABSTRACT:
PROVIDER: PRJEB48133 | ENA |
REPOSITORIES: ENA
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Project description:Salinity stress induces ionic and osmotic imbalances in rice plants that in turn negatively affect photosynthesis rate, resulting in growth retardation and yield penalty. Efforts have, therefore, been carried out to understand the mechanism of salt tolerance, however, the complexity of biological processes at proteome levels remains a major challenge. Here, we performed a comparative proteome and phosphoproteome profiling of microsome enriched fractions of salt-tolerant (cv. IR73; indica) and salt-susceptible (cv. Donjin; japonica) rice varieties. This approach led to the identification of 5,856 proteins, of which 473 and 484 proteins showed differential modulation between DJ and IR sample sets, respectively. The phosphoproteome analysis led to the identification of a total 10,873 phosphopeptides of these 2,929 and 3,049 significant phosphopeptides were identified in DJ and IR sample sets, respectively. The integration of proteome and phosphoproteome data showed activation of ABA and Ca2+ signaling components exclusively in IR in response to salt stress. Taken together, our results highlight the changes at proteome and phosphoproteome levels and provide a mechanistic understand of salt stress tolerance in rice.
2024-12-16 | PXD053678 | Pride
Project description:The aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively. The number of differentially expressed genes was drastically reduced to 70 and 30, by pooling the RNAs from ten extreme tolerant and ten extreme susceptible RILs due to normalization of irrelevant differentially expressed genes between the parents.
2010-04-20 | GSE16108 | GEO
Project description:The aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively. The number of differentially expressed genes was drastically reduced to 70 and 30, by pooling the RNAs from ten extreme tolerant and ten extreme susceptible RILs due to normalization of irrelevant differentially expressed genes between the parents. RNA from CSR27, MI48, tolerant bulk and susceptible bulk grown under control and salt stress conditions were analysed in two different biological replications (A and B) making total sixteen samples
2010-04-28 | E-GEOD-16108 | biostudies-arrayexpress
Project description:Roots make the first contact with the soil environment and are the first responders of stress. These root behaviors are quantifiable and adaptive. The response of rice varieties in mechanical and salinity stress was measured in a novel experimental setup that mimics the soil environment. We analyzed the response of roots by means of SAC (Stress Adaptation Coefficient) in 28 rice varieties that include high-yield salt tolerant varieties as well as geographically isolated native rice varieties. cDNA microarray of IR64 root-tip shows about 6000 common transcripts to be differentially regulated among the two stresses and common pathways were identified. Overall, our study indicates that there is an important commonality in the molecular basis of salt and mechanical stress and presents an easy-to-perform early establishment stress screen for rice varieties.
2018-12-20 | GSE117170 | GEO
Project description:In order to understand molecular mechanisms of salt stress tolerance in rice several researches have been reported, however there are still unclear processes involved in salt tolerance. For reaching to a better perspective of the molecular mechanisms, we designed a comprehensive transcriptome study consisting contrasting genotypes, different tissues and different sampling time points. Two contrasting genotypes were selected and grown in Yoshida hydroponic medium for 14 days under controlled conditions. For salinity stress half of the seedlings were under 150 mM NaCl and after 6 and 54 h the treated and untreated samples were harvested in three replications from roots and shoots separately
2023-01-01 | GSE133480 | GEO
Project description:A submergence tolerant indica rice cultivar FR13A, was also reported to withstand salt stress and proven in our experiments. The mechanism of tolerance is yet to be studied by forward genetics approach. However, it is known that salt stress tolerance is governed by several QTLs and not by a single gene. To understand the mechanism of such a complex mechanism of salt tolerance we selected, two indica rice genotypes namely, I) FR13A, a tolerant indica variety and ii) IR24, a susceptible genotype 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 constitutive and salt stress conditions at seedling stage. Keywords: Mechanism of salt tolerance
2007-12-21 | GSE6600 | GEO
Project description:The aim of this study was to characterize the tissue tolerance mechanisms of rice under salt stress. Our preliminary experiment identified a japonica rice landrace Shuzenji-kokumai (SZK), which is considered to be tissue-tolerant because it can maintain better growth than salt-sensitive rice while having a high Na+ concentration in the shoots under salt stress. These mechanisms differ from those of most salt-tolerant rice varieties, which have low Na+ concentrations in the shoots. We compared the physiological and molecular characteristics of SZK with those of FL478, a salt-tolerant variety, and Kunishi, a salt-sensitive variety. Under salt stress conditions, SZK accumulated high levels of Na+ in roots, leaf sheaths, and leaf blades, which were almost as high as those in the salt-sensitive Kunishi. Simultaneously, SZK maintained better growth and physiological status, as determined by its higher dry weight, lower electrolyte leakage ratio, and lower malondialdehyde concentration. OsNHX1 and OsNHX2 were up-regulated in the leaf sheaths of SZK, suggesting that Na+ is compartmentalized in the vacuole to avoid Na+ toxicity. In contrast, FL478 showed up-regulation of OsHKT1;5 and OsSOS1 in the roots, which exclude Na+ from the shoots. RNA-seq analysis showed that 4623 and 1998 differentially expressed genes (DEGs) were detected in the leaf sheaths and leaf blades of SZK, respectively. Among them, the HSP (heat shock protein) gene expression was highly up-regulated only in SZK, indicating that SZK protects against the protein damage caused by Na+ toxicity. Our findings suggest that SZK has atypical survival mechanisms under salt-stress conditions. These mechanisms offer potential traits for improving salt tolerance in rice.
2024-05-08 | GSE266657 | GEO
Project description:Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties. Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops.
2020-05-09 | GSE150103 | GEO
Project description:The aim of this study is to assess natural variation in transcriptional responses to salt stress in rice. We utilized a diversity panel (RDP1) described in Zhao et al 2011. Eight day old rice seedlings were subjected to a gradual 6 dS·m-1 salt stress for a period of 24h. RNA seqeuncing was performed on shoot tissue using Illumina HiSeq 2500.
2018-01-01 | GSE98455 | GEO
Project description:Rice is one of the main raw materials for Baijiu fermentation and plays an important role in the process of Baijiu brewing. Different varieties of rice may have different compositions of aroma substances in Baijiu due to different contents of physical and chemical components (amylopectin, tannin, fat, etc.), which may affect liquor quality. However, there is currently no systematic understanding of the differences in the types and contents of physicochemical components among different varieties of rice. This study mainly uses modern technological methods to conduct in-depth analysis and precise determination of the physicochemical components of different rice varieties, exploring the differences in physicochemical components of different rice varieties. This study will lay the foundation for the directional breeding of rice for liquor making, and strongly promote the Baijiu industry to accurately screen rice raw materials with higher quality and adaptability.
2024-12-22 | PXD059140 |