Expression data of 8 rice accessions under cold stress in seedling stage
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE71680 | GEO | 2015/10/01
SECONDARY ACCESSION(S): PRJNA291847
REPOSITORIES: GEO
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Project description:Plants from temperate regions can be primed by exposure to low, non-freezing temperatures resulting in improved freezing tolerance. Whereas the molecular and metabolic basis of cold priming has been investigated in detail, hardly anything is known about memory of a previous cold event under warm conditions and a following low temperature triggering event. We show that three days of cold priming at 4°C, a seven-day lag phase at 20°C and a triggering treatment of 4°C improved the freezing tolerance of Arabidopsis Col-0 and other accessions compared to plants that were not primed before. Transcripts, metabolites and lipids as possible molecular determinants of this increase in freezing tolerance were investigated in Arabidopsis accessions Col-0 and N14 after priming, memory phase and triggering by Illumina-based RNA-Seq, GC-MS metabolite profiling and UPLC FT-MS-based lipidomics. Comparing primed and triggered with only triggered samples 93 and 128 unique differentially expressed genes could be identified in Col-0 and N14, together with three and six significantly changed lipids and one metabolite in N14. Possible functions of these candidates will be discussed. This work identified for the first time molecular and metabolic changes accompanying cold stress memory and triggering by a second cold stress.
2019-01-31 | GSE112225 | 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: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: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.
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Project description:Exposure to cold conditions is a major abiotic stress affecting crop growth and productivity. Elucidation of genetic mechanisms underlying response to low temperature is needed. To assess the relationship between the genes and the cold tolerance of wheat, transcriptomics analyses were performed to study changes in gene profiles of cultivar Jing 411 after cold acclimation and freezing treatment. The wheat cultivar Jing 411 was subjected to transcriptome sequencing. The RNA was sequenced on a HiSeq 2500 platform, and the generated data were analyzed using TopHat v2.0.
2019-08-07 | GSE135474 | GEO
Project description:The cold acclimation process is regulated by many factors like ambient temperature, day length, light intensity, or hormonal status. Experiments with plants grown under different light-quality conditions indicate that the plant response to cold is also a light-quality-dependent process. Here, the role of light quality in the cold response was studied in one-month-old Arabidopsis thaliana (Col‐0) plants exposed for one week to 4 °C at short‐day conditions under white (100 and 20 μmol m‐2s‐1), blue or red (20 μmol m‐2s‐1) light conditions. An upregulated expression of CBF1, an inhibition of photosynthesis, and an increase in membrane damage showed that blue light enhanced the effect of low temperature. Interestingly, cold-treated plants under blue and red light showed only limited freezing tolerance compared to white light cold-treated plants. Next, the specificity of the light quality signal in cold response was evaluated in Arabidopsis accessions originating from different and contrasting latitudes. In all but one Arabidopsis accessions, blue light increased the effect of cold on photosynthetic parameters and electrolyte leakage. This effect was not found for Ws-0, which lacks functional CRY2 protein, indicating its role in the cold response. Proteomics data confirmed significant differences between red and blue light treated plants at low temperature and showed that the cold response is highly accession specific. In general, blue light increased mainly the cold-stress related proteins and red light induced higher expression of chloroplast-related proteins, which correlated with higher photosynthetic parameters in red light cold-treated plants. Altogether, our data suggest that light modulates two distinct mechanisms during the cold treatment - red light driven cell function maintaining program and blue light activated specific cold response. The importance of mutual complementarity of these mechanisms was demonstrated by significantly higher freezing tolerance of cold-treated plants under white light.
2022-06-14 | PXD033102 | Pride
Project description:We have sequenced messenger RNA isolated from seedling tissue for 19 accessions of Arabidopsis thaliana (with biological replication). The 19 accessions for which RNA-Seq reads were collected have served as the founders for the MAGIC lines, a high-resolution recombinant inbred line mapping resource. RNA sequencing data was used to examine differential gene expression among the accessions.
2011-08-29 | GSE30720 | GEO
Project description:Leaf rolling and discoloration are two chilling injury symptoms that are widely adopted as indicators for evaluation of cold tolerance at the seedling stage in rice, respectively. However, their relationship has not been well investigated, in particular the mechanism on how low temperature causes leaf rolling at a genome-wide level. In this study, a cold-tolerant japonica cultivar Lijiangxintuanheigu and a cold-sensitive indica cultivar Sanhuangzhan-2 were subjected to different low temperature treatments and physiological and genome-wide gene expression analysis were conducted. Our results showed that leaf rolling happened at temperatures lower than 11℃, but discoloration appeared at moderately low temperatures, such as 13℃. Chlorophyll contents of the two cultivars significantly decreased under 13℃, but didn’t change under 11℃. Contrastly, their relative water contents and the relative electrolyte leakages decreased significantly. Genome-wide gene expression profiling of LTH revealed that the calcium signaling related genes and the genes related to ABA degradation significantly changed under 11℃. Moreover, numerous genes in DREB, MYB, bZIP, NAC, Zin finger, bHLH, WRKY gene families were differently expressed. Furthermore, many aquaporin genes, the key genes in trehalose and starch synthesis were down-regulated under 11℃. These results suggest that the two chilling injury symptoms are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways, and subjected to regulation of multiple transcription regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress result in reduction of water potential in cells and consequently, leaf rolling.
2019-03-30 | GSE112547 | GEO
Project description:During cold acclimation plants increase their freezing tolerance in response to low non-freezing temperatures. This is accompanied by many physiological, biochemical and molecular changes that have been extensively investigated. In addition, many cold acclimated plants become more freezing tolerant during exposure to mild, non-damaging sub-zero temperatures. There is hardly any information available about the molecular basis of this adaptation. However, Arabidopsis thaliana is among the species that acclimate to sub-zero temperatures. This makes it possible to use the molecular and genetic tools available in this species to identify components of sub-zero signal transduction and acclimation. Here, we have used microarrays and a qRT-PCR primer platform covering 1880 genes encoding transcription factors to monitor changes in gene expression in the accessions Columbia-0, Rschew and Tenela during the first three days of sub-zero acclimation at -3°C. The results indicate that gene expression during sub-zero acclimation follows a tighly controlled time-course. Especially AP2/EREBP and WRKY transcription factors may be important regulators of sub-zero acclimation, although the CBF signal transduction pathway seems to be less important during sub-zero than during cold acclimation. Globally, we estimate that approximately 5% of all Arabidopsis genes are regulated during sub-zero acclimation. Particularly photosynthesis-related genes were down-regulated and genes belonging to the functional classes of cell wall biosynthesis, hormone metabolism and RNA regulation of transcription were up-regulated. Collectively, these data provide the first global analysis of gene expression during sub-zero acclimation and allow the identification of candidate genes for forward and reverse genetic studies into the molecular mechanisms of sub-zero acclimation. We used whole genome microarrays to monitor changes in gene expression in the Arabidopsis thaliana accessions Columbia-0, Rschew and Tenela during three days of acclimation to sub-zero temperature at -3°C after cold acclimation
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