Transcriptome profiling of short-term response to chilling stress in resistant and susceptible rice seedlings
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ABSTRACT:
PROVIDER: PRJEB22031 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2061590_1.fastq.gz | Fastqsanger.gz | |||
| ERR2061590_2.fastq.gz | Fastqsanger.gz | |||
| ERR2061600_1.fastq.gz | Fastqsanger.gz | |||
| ERR2061600_2.fastq.gz | Fastqsanger.gz | |||
| ERR2061591_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this study is to profile the short-term transcriptional response of rice to chilling at different timings, and to identify genes that are putatively responsible for stress-tolerance. Thaibonnet and Volano were selected as susceptible and resistant rice cultivars, respectively. According to bibliography and to our quantitative PCR experiment results, we inferred that 2 and 10 hours after the beginning of stress are the time-points in which short-term early and late transcriptional response to chilling is more evident. RNA from Thaibonnet and Volano plants after 0 (not stressed), 2 and 10 hours at 10C were extracted and sequenced. Differential short-term responses to low temperatures at two different timings (to which we refer as early and late) between those two cultivars were analysed by RNA-seq. Our study may contribute to elucidate the molecular mechanisms involved in rice response to chilling and to identify novel genes putatively involved in low temperature tolerance.
2017-10-13 | E-MTAB-5941 | biostudies-arrayexpress
Project description:Transcriptome profiling of short-term response to chilling stress in resistant and susceptible rice seedlings
2019-01-10 | E-MTAB-5941 | ExpressionAtlas
Project description:Chilling is a major stress which adversely decreases photosynthesis and leads to oxidative stress in thermophilic plants. The role of melatonin (MT) in stress response of plants, has so far been investigated, while the mechanisms by which MT regulate photosynthesis in chilling-sensitive cucumber under chilling stress remain unclear. In this paper, we reported MT positively regulated chilling tolerance of cucumber. Moreover, MT showed a concentration-dependent manner and 1.0 μmol·L-1 was the optimum concentration, of which the chilling injury index, EL and MDA were the lowest, while growth was the highest among all the treatments. Further studies indicated that MT triggered the activity and expression of the antioxidant enzymes, which in turn decreased ROS accumulation caused by chilling stress. Meanwhile, MT maintained a high photosynthetic carbon assimilation capacity, increased the activity of PSI reaction center, PSII reaction center and electron transfer efficiency. More importantly, the proteome analysis and western-blot data revealed that PSI-associated proteins (PsaD, PsaE, PsaF, PsaH and PsaN), PSII-associated protein D1 as well as Rubisco large subunit and RCA were significantly up-regulated in MT-treated seedlings, compared to H2O-treated seedlings under chilling stress. These results suggest that MT enhances chilling tolerance of cucumber via activating the antioxidant system as well as protein level of key PSI-, PSII-related and carbon assimilation enzymes to decrease ROS accumulation, and finally alleviates the damage to photosynthetic apparatus under chilling stress.
2022-02-15 | PXD029134 | Pride
Project description:Shoot tips of Cabernet Sauvignon were exposed to chilling, salinity or dehydration (PEG) for short durations.
2010-08-09 | PRD000218 | Pride
Project description:Chilling stress is a major abiotic stress that affects rice growth and development. Rice seedlings are quite sensitive to chilling stress and this harms global rice production. Comprehensive studies of the molecular mechanisms for response to low temperature are of fundamental importance to chilling tolerance improvement. The number of identified cold regulated genes (CORs) in rice is still very small. Circadian clock is an endogenous timer that enables plants to cope with forever changing surroundings including light–dark cycles imposed by the rotation of the planet. Previous studies have demonstrated that the circadian clock regulates stress tolerances in plants show circadian clock regulation of plant stress tolerances. However, little is known about coordination of the circadian clock in rice chilling tolerance. In this study, we investigated rice responses to chilling stress under conditions with natural light-dark cycles. We demonstrated that chilling stress occurring at nighttime significantly decreased chlorophyll content and photosynthesis efficiency in comparison with that occurring at daytime. Transcriptome analysis characterized novel CORs in indica rice, and suggested that circadian clock obviously interferes with cold effects on key genes in chlorophyll (Chl) biosynthesis pathway and photosynthesis-antenna proteins. Expression profiling revealed that chilling stress during different Zeitberger times (ZTs) at nighttime repressed the expression of those genes involved Chl biosynthesis and photosynthesis, whereas stress during ZTs at daytime increases their expression dramatically. Moreover, marker genes OsDREBs for chilling tolerance were regulated differentially by the chilling stress occurring at different ZTs. The phase and amplitude of oscillation curves of core clock component genes such as OsLHY and OsPRR1 are regulated by chilling stress, suggesting the role of chilling stress as an input signal to the rice circadian clock. Our work revealed impacts of circadian clock on chilling responses in rice, and proved that the effects on the fitness costs are varying with the time in a day when the chilling stress occurs.
2022-03-01 | GSE146174 | GEO
Project description:Transcriptome analysis of BPH-resistant and BPH-susceptible rice seedlings in response to BPH infestation. RH vs. 02428: a microarray analysis of genes that were differentially expressed in a BPH-resistant cultivar, Rathu Heenati (RH) and a susceptible cultivar 02428 after infestation with BPH for 24h. RB vs. SB: a microarray analysis of genes that were differentially expressed in resistant seedling pool and susceptible seedling pool both infested with BPH for 24h. RB vs. RN: a microarray analysis of genes that were differentially expressed in resistant seedling pool infested with BPH for 24h and resistant seedling pool without BPH infestation. Goal was to explore the molecular basis underlying BPH-resistance in rice.
2019-11-19 | GSE140562 | GEO
Project description:To understand the molecular mechanisms underlying chilling tolerance in rice, transcriptomic deep sequencing was performed to reveal the differentially expressed genes between chilling tolerance chromosome substitution line (CSL), DC90 and its chilling-sensitive recurrent parent 9311 under early chilling stress events. Our results revealed a set of DEGs with higher basal expression in DC90 by comparison with 9311. They were functionally enriched in GO terms, such as, response to stress, response to stimulus, and response to abiotic stimulus, suggesting their positive role in intrinsic chilling tolerance. Common up-regulated and down-regulated DEGs were enriched in 26 and 34 GO terms, including response to stimulus, response to stress, and response to abiotic stimulus, respectively. Furthermore, comparative transcriptomic analysis between DC90 and 9311 in response to early chilling stress revealed 502 DEGs specifically identified in DC90. Most of gene loci were located beyond introgressed regions, implying that the introgression led to reprogramming of transcriptome in response to early chilling stress. CARMO platform analysis of these DEGs presented a complex regulatory network, including phytohormone signaling, photosynthesis pathway, that coordinately involved in chilling tolerance response of DC90. Here, the unveiled molecular regulatory network shed light on deep understanding the mechanisms of rice chilling tolerance. As well, chilling tolerant-QTLs and co-localized DEGs in introgressed fragments, will be focused for further functional investigation of the molecular mechanisms of early chilling stress response in rice.
2017-06-25 | GSE76415 | GEO
Project description:RNA-Seq was performed to study the change of gene expression before and after chilling treatment in rice. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 15-day-old rice seedlings with and without chilling treatment (4 °C for 33 h) were generated by deep sequencing using Illumina Hiseq 2000 platform.
2016-04-13 | E-GEOD-67373 | biostudies-arrayexpress
Project description:Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in LTH, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in LTH and strong repression in IR29. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. In present study, comprehensive gene expression using an Affymetrix rice genome array revealed a diverse global transcription reprogramming between two rice genotypes under chilling stress and subsequent recovery conditions. The dominant change in gene expression at low temperature was up-regulation in the chilling-tolerant genotype and down-regulation in the chilling-sensitive genotype. Early responses to chilling stress common to both genotypes featured up-regulated genes related to transcription regulation and signal transduction, while functional categories of LR-chilling regulated genes were clearly diverse with a wide range of functional adaptations. At the end of the chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovery capacity at the transcriptional level. Finally, analysis of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, are involved in chilling stress tolerance.
2012-12-21 | GSE38023 | GEO
Project description:The central role of transcriptional regulation in integrating various low temperature response mechanisms has been established in Arabidopsis, where the CBF/DREB regulon plays a prominent role during acclimation. Rice is sensitive to chilling but many japonica cultivars can survive continuous exposure to as low as 10oC for up to 7 days during the most critical stage of seedling establishment better than most indica cultivars. The transcriptional regulatory networks that define this variation have not been studied in detail as cold acclimation has been scrutinized in Arabidopsis. Towards the comparison of the compositional complexity of low temperature response regulons of rice and Arabidopsis, we used the cultivar Nipponbare for genome-wide survey of regulatory clusters by integrative analysis of promoter architectures and temporal expression profiles during exposure to 10oC at narrow time intervals. Temporal profiles revealed major clusters of genes that were induced within the initial 24 hours. These clusters were further defined by common features of having either CRT/DRE-like elements, as1/ocs-like elements or both in their promoters. Genes containing as1/ocs-like elements with or without CRT/DRE, but not those containing only CRT/DRE-like elements were induced by exogenous H2O2 but not by ABA at ambient temperature, suggesting that they belong to a potential regulon (ROS-bZIP – as1/ocs module) that responds to elevated levels of reactive oxygen species (ROS) during the initial stages of stress. Parallel analysis of transcription factors during the initial 12 hours revealed candidate regulator(s) of this putative early response regulon. Cultivar-specific expression signatures of selected members of this regulatory cluster were also positively correlated with genotypic variation in chilling tolerance. We hypothesized that the ROS-bZIP – as1/ocs cluster has important roles in configuring the transcriptome of rice seedlings during the early stages of chilling stress and it appears to be independent of ABA and functions in parallel to the CBF/DREB regulon. Keywords: time course (response to low temperature)
2009-12-31 | GSE8767 | GEO