Ontology highlight
ABSTRACT:
PROVIDER: PRJNA926808 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23230480_1.fastq.gz | Fastqsanger.gz | |||
| SRR23230480_2.fastq.gz | Fastqsanger.gz | |||
| SRR23230482_1.fastq.gz | Fastqsanger.gz | |||
| SRR23230482_2.fastq.gz | Fastqsanger.gz | |||
| SRR23230483_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Genome-wide transcriptome analysis was performed to understand the expression pattern of transcriptomes in tolerant and susceptible subtropical maize genotypes under waterlogging stress condition. Waterlogging stress causes yield reduction in maize (Zea mays). It is important to dissect the genetic circuits that underlie the plant responses to waterlogging. So, the experiment was designed with the following objectives: to understand the expression pattern of transcriptomes in the tolerant and the susceptible genotypes under waterlogging stress; to identify DEGs functioning in important pathways underlying adaptive traits; to co-map bin locations of the transcriptomes with already known QTLs for waterlogging and find synteny with other species; and to generate gene co-expression networks to study cohorts of genes expressed together in modules and functional cluster, while comparing the two genotypes.
2013-08-14 | GSE43088 | GEO
Project description:Genome-wide transcriptome analysis was performed to understand the expression pattern of transcriptomes in tolerant and susceptible subtropical maize genotypes under waterlogging stress condition. Waterlogging stress causes yield reduction in maize (Zea mays). It is important to dissect the genetic circuits that underlie the plant responses to waterlogging. So, the experiment was designed with the following objectives: to understand the expression pattern of transcriptomes in the tolerant and the susceptible genotypes under waterlogging stress; to identify DEGs functioning in important pathways underlying adaptive traits; to co-map bin locations of the transcriptomes with already known QTLs for waterlogging and find synteny with other species; and to generate gene co-expression networks to study cohorts of genes expressed together in modules and functional cluster, while comparing the two genotypes. Two tropical maize (Zea mays L.) inbred lines, HKI1105 (tolerant) and V-372 (susceptible), were used for our experiment. The genotypes were sown in plastic pots filled with loam soil with sandy texture. The plants were watered daily to soil capacity until the application of stress at 28 days after sowing. To impose waterlogging condition, the perforation in the bottom of the pots (35 cm in height) was sealed and the stress treatment was given by watering the pots (5 cm standing water) for seven continuous days. To allow for recovery from stress, the perforations of the pots were unsealed for proper drainage of excess water. The root samples from both genotypes were collected on the 28th, 32nd, 35th and 42nd day after sowing, which represented control, moderate stress, severe stress and post-stress recovery stages, respectively. Two biological replications were used for each comparison.
2013-08-14 | E-GEOD-43088 | biostudies-arrayexpress
Project description:Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding of the effect of waterlogging stress in barley, we carried out a genome-wide gene expression analysis in roots of Yerong and Deder2 barley genotypes under waterlogging and control (well-watered) conditions by RNA-Sequencing, using Illumina HiSeq™ 4000 platform.
2020-02-14 | GSE144077 | GEO
Project description:Purpose: To gain a better understanding of the molecular mechanisms that enable de novo AR primordia emergence upon waterlogging, the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, Zaoer-N (waterlogging tolerant) and Pepino (waterlogging sensitive), which differed in their abilities to form AR were compared. Conclusion: This research broadens our understanding of the mechanism underlying waterlogging-triggered ARs emergence, and provides valuable information for the breeding of cucumber with enhanced waterlogging tolerance.
2022-04-29 | GSE130467 | GEO
Project description:A customized targeted oligoarray was used to monitor the expression levels of 1000 genes, representative of the immature kernel transcriptome. Using this oligoarray we compared transcripts from 10 DAP kernels of two susceptible and two drought tolerant genotypes. These four genotypes were extracted from our RIL population (B73xH99) and grown under water stress and well watered field conditions. Keywords: Stress response Two-condition experiment: water stress field condition vs. well watered field condition. Transcriptional profiling of 10 DAP kernel (two susceptible and two drought tolerant genotypes) in the first condition vs 10 DAP kernel (two susceptible and two drought tolerant genotypes) in the second condition. Hybridization replicates: 4 in dye swap mode. Two probes per gene per array.
2008-12-21 | E-GEOD-11568 | biostudies-arrayexpress
Project description:Genome-wide transcriptome analysis was performed to understand the expression pattern of transcriptomes in tolerant and susceptible subtropical maize genotypes under water deficit stress condition.<br><br>
2014-10-11 | E-MEXP-3992 | biostudies-arrayexpress
Project description:Background: Soil salinity is a major abiotic stress factor that limit agricultural productivity worldwide, and this problem is expected to grow in the future. Common bean (Phaseolus vulgaris L.) is an important protein source in developing countries is highly susceptible to salt stress. To understand the underlying mechanism of salt stress responses, transcriptomics, metabolomics, and ion content analysis were utilized for response comparison of salt-tolerant and salt-susceptible common bean genotypes in saline conditions. Results: Transcriptome analysis has revealed that the tolerant genotype had increased photosynthesis in saline conditions while the susceptible genotype acted in a contrasting way. The chlorophyll content measurements have backed up this result with increase in tolerant and decrease in susceptible genotype. Transcriptome also displayed a more active carbon and amino acid metabolism for the tolerant genotype as well. Analysis of primary metabolites with GC-MS demonstrated the boosted carbohydrate metabolism in the tolerant genotype with increased sugar content as well as better amino-acid metabolism with the accumulation of glutamate and asparagine and hinted a lowered photorespiration level for the tolerant one. Accumulation of lysine, valine, and isoleucine in the roots of the susceptible genotype suggested a halted stress response pathway. According to ion content comparison, the tolerant genotype managed to block accumulation of Na+ in the leaves while accumulating significantly less Na+ in the roots compared to susceptible genotype. K+ levels increased in the leaves of both genotype and the roots of the susceptible one but dropped in the roots of the tolerant genotype. Additionally, Zn+2 and Mn+2 levels were also dropped in the tolerant roots, while Mo+2 levels were significantly higher in all tissues in both control and saline conditions for tolerant genotype. Conclusion:The results of the presented study have demonstrated the differences in contrasting genotypes and thus provide valuable information on the pivotal molecular mechanisms underlying salt tolerance mainly in common bean, but for all crops.
2020-11-20 | GSE156113 | GEO
Project description:‘Hangju’ is a variety of Chrysanthemum morifolium Ramat with both aesthetic and medicinal value, cultivated as traditional Chinese medicine for four centuries. The cultivation of ‘Hangju’ faces a significant challenge due to waterlogging stress, resulting in a considerable decrease in crop yield. Nevertheless, there is a scarcity of studies exploring the underlying mechanisms of waterlogging tolerance in ‘Hangju’. This investigation focused on comparing the characteristics of the waterlogging-tolerant variety EWT and the waterlogging-sensitive variety CK of ‘Hangju’. The study revealed that EWT exhibited a more advanced aeration tissue structure and demonstrated rapid development of adventitious roots following waterlogging. Through a time-course transcriptome analysis, it was observed that EWT could swiftly adjust the expression of genes involved in energy metabolism signaling pathways to acclimate to the waterlogged environment. WGCNA analysis identified INTEGRASE-TYPE DNA-BINDING PROTEIN (CmTINY2) as a key factor in regulating waterlogging tolerance in EWT. CmTINY2, a transcription factor belonging to the ethylene responsive factor (ERF) subfamily III, operated within the nucleus and activated downstream gene expression. Its role in enhancing waterlogging tolerance might be linked to the control of stomatal aperture. In summary, this research has elucidated that the waterlogging tolerance exhibited by EWT chrysanthemum is a result of a combination of morphological structure and molecular regulatory mechanisms. Furthermore, the discovery of a waterlogging-tolerant gene from the ERF subfamily III has broadened our understanding of the role of ERF genes in waterlogging signaling pathways.
2024-06-11 | GSE269106 | GEO
Project description:To investigate the salt and waterlogging mechanism of barley, we chose salt and waterlogging sensitive and tolerant varieties as subjects. We then performed gene expression profiling analysis using data obtained from RNA-seq of two varieties at two three points.
2023-05-31 | GSE230751 | GEO
Project description:‘Pulsechip’, a boutique cDNA microarray, generated from a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) ESTs and lentil (Lens culinaris Med.) resistance gene analogs, was employed to generate an expression profile of chickpea accessions tolerant and susceptible to high-salinity stress. Two groups of a tolerant and susceptible accession were challenged with high-salinity stress. The experiments were performed in three biological replications. The experiments were conducted in reference design where respective tissues from unstressed plants served as control. The leaf/shoot and root tissues were collected at 24 and 48 h post-treatment (hpt) and used for hybridization to measure changes in RNA abundance of treatment vs. control. The tissues from five experimental replicate plants per biological replication were pooled together (shoot and root tissues separate for each time point) before RNA extraction. This RNA was used to prepare cDNA targets for expression analysis using microarray. The microarray had six technical replicate spots per EST. The transcript level for each EST/cDNA was firstly calculated as the average intensity of the six technical replicates and then the average intensity of three biological replicates. Data analysis included LOWESS normalization (LOcally WEighted polynomial regreSSion) to adjust for differences in quantity of initial RNA, labeling and detection efficiencies. A dye swap in one biological replicate adjusted dye bias, if any. The Differentially Expressed (DE) ESTs were identified as those with a 95% confidence interval for mean fold change (FC) that extended beyond the two-fold cut-off and also passed the Students t test (P<0.05) and FDR correction. These cut-offs translate into induced ESTs having a log2 ratio > 1 and repressed ESTs a ratio of < -1. The analysis consisted of three fold comparison. Firstly, the ESTs that were differentially expressed between treatment and control plants of each accession were detected. Then the ESTs that were similarly expressed by tolerant and susceptible accessions were then eliminated by comparison. This included a two-way comparison, where tolerant and susceptible genotypes were compared within and between groups. Lastly, ESTs that were consensually differentially expressed between tolerant and susceptible accessions of the two batches were identified. The hypothesis was that if a putative gene was consistently expressed only in tolerant or susceptible genotype for a particular stress, it might be a candidate for tolerance/susceptibility for that stress. Globally, the level of 409 transcripts was affected in response to high-salinity stress in all the genotypes and tissue types studied. Of the transcripts consistently expressed in tolerant genotypes in response to high-salinity stress, the annotation of transcripts at 24 hpt suggest a reduction in energy production in shoots and roots by repression of putative genes including P700 chlorophyll a-apoprotein (DY475501) and NADH-plastoquinone oxidoreductase subunit I (DY475287), cytosolic fructose 1,6-bisphosphatase (DY475548) and splicing factor-like protein (DY396290). The ATHP3 (DY396300) and protein kinase (DY475077) that are potentially involved in signalling cascades responsible for sensing and relaying osmotic stress signals, were consistently repressed in tolerant genotypes in response to high-salinity. Additionally a glycine rich protein (DY396342) that is associated with lignification of cell walls in response to wounding and pathogen attack was repressed in tolerant genotypes. In tolerant genotypes at 48 hpt, two energy and metabolic-related transcripts were consistently repressed in roots, including a carbonic anhydrase (DY475403) and putative thiazole biosynthetic enzyme (DY475242). In shoots, only a pathogenesis-related protein (DY396301) was consistently repressed at 48 hpt, but a similar transcript (DY396281) was induced in roots of tolerant genotypes at the same time. Only four transcripts were DE in susceptible genotypes at 24 hpt, all occurring in root tissue. Two of these were unknown/unclear, but the others included a proline oxidase transcript (DY475225) and a nuclear transport factor 2 (DY396436). At 48 hpi, a putative splicing factor-like protein (DY396290) and polyubiquitin (DY396328) were repressed in roots of susceptible genotypes. Interstingly, a putative xylosidase (DY475408) was induced in susceptible roots at 48 hpi. Finally, several unknown/unclear transcripts were DE in both tolerant and susceptible genotypes. Of interest were two unknowns (DY475293 and DY475521) that were consistently expressed in tolerant genotypes and may be important for high-salinity tolerance. Keywords: Chickpea, High-salinity stress, tolerant, susceptible, cDNA microarray
2007-04-03 | GSE7418 | GEO