Oryza sativa ssp. japonica (Kitaake) stressed by cold stress (5°C, 24 h) targeted to leaves (C-L), roots (C-R) or the whole plant (C), and exposed to previous acclimation (15°C, 12 h)
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE246145 | GEO | 2024/01/01
REPOSITORIES: GEO
Similar Datasets
Project description:To stabilize crop yield under low temperature stress conditions, it is important to improve stress tolerance in crops. Upon exposure to low temperature stress, many genes are induced and their products are thought to function as cellular protectants of stress-induced damages Therefore, responses of global gene expression profiles to cold stress was analyzed at the booting stage using the 60K Rice Whole Genome Microarray. The cold-tolerant rice variety, Stejaree45 was transplanted in 1/5000 pot at 20 days after seeding. Fertilizers were applied at the rate of 11, 7.7 and 9.3 kg/10a in N, P2O5 The samples were selected at the booting stage of rice on the basis of the auricle distance (the distance between auricles of flag leaf and the previous leaf of the main culm). The plants with an auricle distance ranging from -5 ㎝ to 0 ㎝ were exposed up to the flag leaf auricle using cold water (13℃) for 3 days. Glumous flowers and flag leaves of the cold-resistant variety, Stejaree45, were used to examine gene expression profiles.
2010-12-08 | E-GEOD-19389 | biostudies-arrayexpress
Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.
2016-01-13 | GSE73181 | GEO
Project description:In the field, abiotic stresses are rarely applied individually. Crops are often subjected to a combination of stresses. To date, no study has been performed on the proteomic investigation of the response of common wheat to a combination of drought and cold stresses. In this study, wheat seedlings exposed to drought-cold stress for 24 h showed inhibited growth, increased lipid peroxidation, relative electrolyte leakage, and soluble sugar contents. To determine the wheat protein response to drought-cold stress, iTRAQ-based quantitative proteomic and liquid chromatography tandem mass spectrometry (LC-MS/MS) methods were employed to determine the proteomic profiles of the roots and leaves of wheat seedlings exposed to drought-cold stress conditions. We identified 250 and 258 proteins with significantly altered abundance in the roots and leaves, respectively. These proteins were classified into several main groups, as follows: protein metabolism, stress/defense, carbohydrate metabolism, lipid metabolism, transcription-related processes, energy production, cell-wall and cytoskeleton metabolism, membrane and transportation, signal transduction, other metabolic processes, and unknown biological processes. Nine proteins were simultaneously presented in both roots and leaves exposed to drought-cold stress, and the majority of proteins identified differed from one another and displayed differently altered abundance. These findings uncovered organ-specific differences in adaptation to drought-cold stress. Exogenous abscisic acid (ABA) application conferred the plant with protection against drought-cold stress and significantly increased catalase and peroxidase enzyme activities, as well as the transcription of glutathione S-transferase and other 11 sample genes in the roots or leaves, respectively. These results suggested that ABA is a potentially vital factor that contributes to the drought-cold signaling pathway and a promising target for growth recovery. Furthermore, VIGS (virus-induced gene silencing)-treated plants generated for three candidate protein genes TaGRP2, CDCP and WCOR410c were subjected to drought-cold limitation, they showed more serious droop and wilt, increased rate of relative electrolyte leakage, and reduced relative water content (RWC) compared to viral control plants. These results may indicate that TaGRP2, CDCP and WCOR410c play important roles in conferring drought-cold tolerance in wheat. These findings can provide useful insights into the molecular mechanisms of drought-cold responses in higher plants.
2018-05-17 | PXD004396 | Pride
Project description:Low temperature is one of the major abiotic stresses limiting rice growth and productivity, it is urgent to reveal the genetic and molecular mechanisms of plant responses to low temperature stress and to search for useful genetic resources for improving low-temperature tolerance. the 8 accessions from China Core Collection include 4 cold tolerance accessions, 3 sensitivity accessions and 1 intermediate type accession. We used microarrays to detail variation of the gene expression after cold treatment and screen more cold-response genes in rice.
2015-10-01 | GSE71680 | GEO
Project description:To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative “omic” approaches were applied to F. ananassa ‘Korona’. Analysis of leaf tissue was emphasized because of its immediate and early responses in the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 20°C were compared to those following 1 to 10 days of cold exposure. When leaves and roots were subjected to GC/TOF-MS-based metabolite profiling, about 160 compounds comprising mostly structurally annotated primary metabolites and secondary metabolites, were found. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine), pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose). Distinctive responses were observed in roots and leaves. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold. Twenty-one proteins were identified, many of which were associated with general metabolism or photosynthesis. Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb) to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature stress change in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant.
2015-09-29 | GSE73488 | GEO
Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice. Leaf and root mRNA profiles of Dongxiang wild rice at the seedling stage with or without salt stress were generated by deep sequencing, on Illumina Hiseq 2000 platform.
2016-01-13 | E-GEOD-73181 | biostudies-arrayexpress
Project description:Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. The cold-tolerant and cold-sensitive genotypes were previously characterized, and are sister lines (derived from the same crossing).
2017-09-06 | GSE103480 | GEO
Project description:Purpose: Rice (Oryza sativa) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the roots of two rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress during the early vegetative stage. Results: RNAseq analysis revealed that contrasting genotypes present a completely different molecular response to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes that might contribute to rice cold tolerance, including the ones related with cell wall remodeling (glycosyl hydrolase, cellulose synthase, glycosyl transferase, wall-associated kinase, glycine-rich cell wall structural protein), cytoskeleton and growth (microtubule-associated protein 70, kinesin motor domain containing protein, growth regulating factor protein, auxin-independent growth promoter protein, RopGEF7), signaling (receptor-like protein kinase, Rapid Alkalinization Factor 21)), antioxidant system (glutathione peroxidase, metallothionein), lipid metabolism (fatty acid desaturase and phosphatidylinositol transfer protein), and stress response (Tetratricopeptide Repeat-Containing Protein). On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Even though these two genotypes have a similar genetic background (sister lines), some of these genes can probably be involved with cold tolerance or sensitivity and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.
2020-02-21 | GSE145582 | GEO
Project description:To stabilize crop yield under low temperature stress conditions, it is important to improve stress tolerance in crops. Upon exposure to low temperature stress, many genes are induced and their products are thought to function as cellular protectants of stress-induced damages Therefore, responses of global gene expression profiles to cold stress was analyzed at the booting stage using the 60K Rice Whole Genome Microarray.
2010-12-08 | GSE19389 | GEO
Project description:Cold stress greatly affects plant growth and crop yield. To identify novel genes and possible mechanisms involved in chilling tolerance responses in rice seedlings, RNA sequencing (RNA-seq) technology was used for genome-wide gene expression profiling analysis to compare three cold-tolerant genotypes and one cold-sensitive genotype under both normal temperature and cold stress treatments.
2013-07-11 | E-MTAB-4407 | biostudies-arrayexpress