Ontology highlight
ABSTRACT:
PROVIDER: PRJNA655825 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12407153_1.fastq.gz | Fastqsanger.gz | |||
| SRR12407153_2.fastq.gz | Fastqsanger.gz | |||
| SRR12407154.fastq.gz | Fastqsanger.gz | |||
| SRR12407154_1.fastq.gz | Fastqsanger.gz | |||
| SRR12407154_2.fastq.gz | Fastqsanger.gz |
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Project description:Drought is a harmful abiotic stress that threatens the growth, development, and yield of rice plants. To cope with drought stress, plants have evolved diverse and sophisticated stress-tolerance pathways by regulating gene expression. Previous genome-wide studies have revealed many rice drought stress-responsive genes that are involved in various metabolism, hormone biosynthesis and signaling pathways, and transcriptional regulation. However, little is known about the regulation of drought-responsive genes during rehydration after dehydration. In this study, we examined the dynamic gene expression patterns in rice seedling shoots during dehydration and rehydration using RNA-seq analysis. To investigate the transcriptome-wide rice gene expression patterns during dehydration and rehydration, RNA-seq libraries were sequenced and analyzed to identify differentially expressed genes (DEGs). DEGs were classified into five clusters based on their gene expression patterns. The clusters included drought-responsive DEGs that were either rapidly or slowly recovered to control levels by rehydration treatment. Representative DEGs were selected and validated using qRT-PCR. In addition, we performed a detailed analysis of DEGs involved in nitrogen metabolism, phytohormone signaling, and transcriptional regulation. In this study, we revealed that drought-responsive genes were dynamically regulated during rehydration. Moreover, our data showed the potential role of nitrogen metabolism and jasmonic acid signaling during the drought stress response. The transcriptome data in this study could be a useful resource for understanding drought stress responses in rice, and may provide a valuable gene list for developing drought-resistant crop plants.
2023-05-17 | GSE222438 | GEO
Project description:Rain-fed plants are subjected to cycles of drought and re-watering. Thus, efficient recovery from drought may be among the key determinants in the success of these plants, yet the mechanisms by which plant recover from drought have been historically understudied. To parse out the specific molecular processes leading to stress recovery, we performed a fine-scale time course of bulk RNA sequencing starting just 15 minutes after rehydration. We revealed that transcriptional drought recovery is an active and rapid process involving activating thousands of recovery-specific genes. To map the immediate recovery responses in diverse leaf-cell-types, we performed a single-nucleus transcriptome analysis of the onset of recovery from long-term moderate drought. Here we show the formation of unique cell states initiated rapidly following plant rehydration. We reveal the activation of a microbial-autonomic induction of the immune system and demonstrate that the onset of recovery leads to increased resistance against pathogens in Arabidopsis (Arabidopsis thaliana), wild tomato (Solanum pennellii) and domesticated tomato (Solanum lycopersicum cv. M82). Our findings uncover that the preventive immune activation was preserved despite extensive selection during tomato domestication. Since rehydration increases microbial proliferation and, thus, the risk for infection, pre-activating immunity may be crucial for plants survival in natural environments. This work lays the foundation for unraveling the complexed processes actively facilitating stress recovery within plant leaves.
2025-07-29 | GSE303744 | GEO
Project description:Rain-fed plants are subjected to cycles of drought and re-watering. Thus, efficient recovery from drought may be among the key determinants in the success of these plants, yet the mechanisms by which plant recover from drought have been historically understudied. To parse out the specific molecular processes leading to stress recovery, we performed a fine-scale time course of bulk RNA sequencing starting just 15 minutes after rehydration. We revealed that transcriptional drought recovery is an active and rapid process involving activating thousands of recovery-specific genes. To map the immediate recovery responses in diverse leaf-cell-types, we performed a single-nucleus transcriptome analysis of the onset of recovery from long-term moderate drought. Here we show the formation of unique cell states initiated rapidly following plant rehydration. We reveal the activation of a microbial-autonomic induction of the immune system and demonstrate that the onset of recovery leads to increased resistance against pathogens in Arabidopsis (Arabidopsis thaliana), wild tomato (Solanum pennellii) and domesticated tomato (Solanum lycopersicum cv. M82). Our findings uncover that the preventive immune activation was preserved despite extensive selection during tomato domestication. Since rehydration increases microbial proliferation and, thus, the risk for infection, pre-activating immunity may be crucial for plants survival in natural environments. This work lays the foundation for unraveling the complexed processes actively facilitating stress recovery within plant leaves.
2025-07-23 | GSE220277 | GEO
Project description:All organisms experience stress as an inevitable part of life, from single-celled microorganisms to complex multicellular beings. The ability to recover from stress is a fundamental trait that determines the overall resilience of an organism, yet stress recovery is understudied. To understand the stress recovery process, we studied the recovery from drought stress in Arabidopsis thaliana. We performed a fine-scale time series of bulk RNA sequencing starting 15 minutes after rehydration following moderate drought. We reveal that drought recovery is a rapid process involving the activation of thousands of recovery-specific genes. To capture these rapid recovery responses in different leaf cell types, we performed single-nucleus transcriptome analysis at the onset of post-drought recovery, identifying a cell type-specific transcriptional state developing independently across cell types. Furthermore, we reveal a recovery-induced activation of the immune system that occurs autonomously, and which enhances pathogen resistance in vivo in A. thaliana, wild tomato (Solanum pennellii) and domesticated tomato (Solanum lycopersicum cv. M82). Since rehydration promotes microbial proliferation and thereby increases the risk of infection, the activation of drought recovery-induced immunity may be crucial for plant survival in natural environments. These findings indicate that drought recovery coincides with a preventive defense response, unraveling the complex regulatory mechanisms that facilitate stress recovery in different plant cell types.
2025-07-23 | GSE289042 | GEO
Project description:Castor is an important industrial raw material. Drought leads to delayed development and reduced yield of castor plants. However, the molecular mechanism of the response of castor plants to drought stress has not been determined. In this study, physiological, biochemical, and RNA-seq analyses were conducted on castor roots under PEG-6000 stress for 3, 7, and 4 d (11 d) of rehydration. The activities of GR, APX, SOD, and CAT in the roots of the castor plants under PEG-6000 stress increased at 3 d and decreased at 7 d, while the activity of POD continued to increase. A total of 2926, 1507, and 111 DEGs were identified in castor roots stressed with PEG-6000 for 3 d and 7 d and rehydrated for 4 d (11 d), respectively. GO analysis revealed that antioxidant activity was significantly enriched under PEG stress. In addition, KEGG enrichment analysis revealed that the DEGs were significantly involved in glutathione metabolism, fatty acid metabolism, and plant hormone signal transduction. KEGG combined with WGCNA was used to screen two drought stress-related genes, PP2C39 and GA2ox4. We propose an oxidative stress model for castor plants under drought stress based on GO terms, KEGG pathway, and WGNA analyses. This study identified high-quality genes for the genetic and molecular breeding of drought-resistant castor beans.
2024-10-23 | GSE252706 | GEO
Project description:To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress and 2hr rehydration, expression profiles of Poly (A+) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed.
2016-07-31 | GSE83846 | GEO
Project description:Drought priming is a promising approach to improve drought tolerance, and root apex plays important role in coping with drought adversities in plants. It has been observed that less inhibition of root growth under drought stress was found in paralleling with the enhanced drought tolerance induced by drought priming in wheat. However, the contribution and mechanisms of root apex to the improved tolerance induced by drought priming remains unknown. Here, the transcriptome and proteome of three different zones along the root axis under drought stress were investigated. The two zones distal from the root apex showed more sensitive to drought priming and the later drought stress than the zone proximal to the root apex, as exemplified by the principal component analysis of the different expressed genes (DEGs) among treatments. The DEGs which decreased by drought stress, while higher expressed in primed plants than non-primed plants, might play critical roles in enhanced root growth in primed plants. These genes were mainly involved in the pathways related to cell membrane sensing, plant hormone signaling, stress defense and cell more modification. Moreover, the plant hormone pathway showed positive correlated between transcriptome and proteome analysis, and genes network analysis hinted that ABA receptor and aquaporin could be potential markers in regulation of priming induced root growth and drought stress tolerance.
2025-07-01 | GSE133921 | GEO
Project description:In order to revael the relationship between gene expression and plant phenotype under drought, we conducted transcriptome analysis under six drought and control conditions.
2023-11-30 | GSE233456 | GEO
Project description:As a major plant abiotic stress, drought stress suppresses crop yield performance severely. However, the trade-off between crop drought tolerance and yield performance becomes a great challenge in drought-resistant crop breeding. Several phytohormones have been reported to participate in plant drought response, including gibberellin (GA), which also plays an important role in plant growth and development. Using CRISPR technology, we constructed the null mutant of ZmGA20ox3, a key enzyme in GA biosynthesis. The null mutant plants show lower plant height and ear height with no yield loss under the normal condition than wild-type plants. Transcriptome analysis revealed that genes affected by ZmGA20ox3 were enriched in signal transduction and stress response processes. In addition to the decrease of GA, a significant increase of ABA and JA level were also detected in mutant plants. Compared with wild-type plants, the growth and ASI of mutant plants were less affected, and the yield loss was also reduced under drought conditions. These results suggest a potential role of ZmGA20ox3 in maize drought response. Our result shows that regulating GA biosynthesis is applicable for maize drought-resistant breeding.
2024-04-10 | GSE229138 | GEO
Project description:Background Drought is a global challenge that severely restricts crop yields and threatens food security. Plants respond to drought stress by modulating gene expression before visible phenotypic changes occur. However, most studies of drought resistance have examined phenotypes after drought treatment, with little emphasis on how severely the plants were perceiving drought-stress conditions before the appearance of stress symptoms. We therefore developed drought-stress biomarkers (DSBMs) to detect drought-stress perception levels based on gene expression profiles by performing time-series transcriptome analysis and phenotypic analysis of rice (Oryza sativa) under drought conditions in the growth chamber. Results Time-series RNA-seq of the drought-susceptible rice cultivar IR64 revealed drastic changes in the transcriptome after 4–6 days of drought treatment in plants grown in pot culture mimicking drought conditions in the field, particularly for genes related to photosynthesis. Among the differentially expressed genes, we selected 23 DSBM genes that consistently responded to drought stress. Rehydration immediately reset the changes in expression of these DSBM genes, indicating that their expression changes reflect current drought-stress perception levels, but not stress memories. Responses of DSBM genes tended to be conserved among rice accessions, irrespective of the rice subpopulation (such as indica, aus, and japonica). We developed a machine learning model using the expression levels of DSBM genes trained by the time-series RNA-seq data for IR64. This model successfully predicted the drought-stress perception levels of various rice accessions, representing the probability of exposure to drought treatment, with an accuracy of 75%. Extreme root architecture traits, such as the largest root surface area, narrowest crown root diameter, and largest ratio of deep rooting, influenced the predicted drought-stress perception levels. Conclusion We identified DSBM genes and developed a machine learning model as a robust tool for assessing drought-stress perception levels in rice. Monitoring and predicting drought-stress perception levels should contribute to more efficient crop management and breeding schemes. Furthermore, our dataset would serve as a resource for further understanding the mechanisms of drought resistance in rice.
2025-07-30 | GSE288615 | GEO