Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1028983 | ENA |
REPOSITORIES: ENA
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Project description:The booting stage of rice shows the most sensitivity to cold stress, and low-temperature stress causes irreversible pollen sterility. We performed transcriptome analysis using RNA-seq to investigate the response of rice anthers to low-temperature stress. In this RNA-seq analysis, to validate the results of transcriptome analysis of anthers from 13 rice lines using microarrays, four cultivars were selected for analysis from the 13 tested for microarrays.
2024-11-29 | GSE270782 | GEO
Project description:The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains.
2013-08-06 | GSE49561 | 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:we utilized transcriptome sequencing to identify differentially expressed genes in rice heat-tolerant line and heat-sensitive line under high night temperature stress .
2023-02-20 | GSE225259 | GEO
Project description:As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment.
2012-02-19 | GSE31077 | GEO
Project description:Here, we investigated the function of the plant-specific SR protein RS33 in pre-mRNA splicing regulation and abiotic stress responses in rice. The loss-of-function mutant, rs33, showed increased sensitivity to salt and low-temperature stress. Genome-wide analyses of gene expression and splicing in seedlings subjected to these stresses identified multiple splice isoforms from stress-responsive genes dependent on RS33. The number of RS33-regulated genes is much higher under low-temperature stress as compared to salt stress. Our results suggest that this plant-specific splicing factor plays crucial and distinct roles during plant adaptation to abiotic stresses.
2022-06-15 | GSE194283 | 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:Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. Japan, especially western and central parts, has seen record high temperatures in the last decade, and the rice kernel quality has decreased; specifically a reduction the first-grade of rice has been seen. In this study, we specifically looked at the harvested rice in a town of the central Kanto-plains (Japan) during the year 2010, which saw day-time temperatures go above the critical limits ranging from 34 to 38C at the final stages of seed development and maturity to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial) were obtained Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki prefecture in September 2010, as grade 1 (labeled as Y1), grade 2 (labeled as Y2), and grade 3 (out-of-grade, labeled as Y3). The research objective was to examine in particular alterations in gene expressions genome-wide in grade 2 (Y2) and grade 3 (Y3) seeds over the grade 1 (Y1) following the high-temperature spike using a high-throughput omic-approach DNA microarray (Agilent 4 x 44K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. Rice seed quality analysis revealed, as expected, low quality in Y3 > Y2 over Y1, in taste, amylose, protein and fatty acid degree, but not in water content. Transcriptome profiling data revealed 124 and 373 up-regulated and 106 and 129 down-regulated genes in Y2 and Y3, respectively. Bioinformatics analysis of differentially expressed genes revealed changes in function of genes related to metabolism, including starch metabolism (e.g., alpha amylase), defense/stress response, fatty acid biosynthesis and hormones. This research provides for the first time the seed transcriptome profile for the classified low grades (2 and out-of-grade) of rice under an actual stressed environmental condition of high temperature.
2016-03-21 | GSE79405 | GEO
Project description:N6-methyldeoxyadenosine (6mA) is a newly-discovered DNA modification that plays a role in regulating plant adaptation to abiotic stresses. However, the changes and molecular regulatory mechanisms of N6-methyldeoxyadenosine under cold stress in plants remain uncertain. Here, we found the global level of 6mA in both Arabidopsis and rice are raised after cold treatment. Genome-wide profiling of 6mA revealed that 6mA peaks are primarily distributed within gene body regions under both normal and low-temperature conditions. Additionally, genes that were up-methylated were enriched in various biological processes, while down-methylated genes did not exhibit any significant enrichment. Association analysis showed that 6mA was positively correlated with gene expression level and 6mA-containing genes displayed a significantly higher expression level than non-6mA-containing genes. Joint analysis of the 6mA methylome and transcriptome of Arabidopsis and rice revealed that the fluctuations in 6mA levels caused by exposure to cold did not correlate with the changes of transcript levels in response to low temperatures. Moreover, we found that 6mA modified orthologous genes exhibit high expression levels. However, upon cold treatment, only a small amount of differentially 6mA-methylated orthologous genes were shared between Arabidopsis and rice. In sum, this study profiled the changes of 6mA in response to cold temperature and has unlocked the potential of this DNA modification in regulating the expression of stress-related genes.
2023-06-19 | GSE230463 | GEO