Comparative RNA-seq based transcriptome profiling of waterlogging response in cucumber hypocotyls
Ontology highlight
ABSTRACT:
ORGANISM(S): Cucumis sativus
PROVIDER: GSE130467 | GEO | 2022/04/29
REPOSITORIES: GEO
Similar Datasets
Project description:Comparative RNA-seq based transcriptome profiling of waterlogging response in cucumber hypocotyls
| PRJNA540302 | ENA
Project description:Cucumber is an important vegetable crop worldwide, which is mainly propagated by seed. The successful occurrence of double fertilization is the premise of seed production in angiosperms. Cucumber ALC homolog (CsALC) displayed a novel and positive function in pollen tube emergence process, and regulated female fertility by promoting CsRALF4/19 function during pollen tube guidance in cucumber.
2023-01-20 | GSE182139 | GEO
Project description:Waterlogging leads to major crop losses globally, particularly for waterlogging sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related QTLs have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging, and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA-sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called ‘core hypoxia response genes’, thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study ‘predisposition’ to waterlogging tolerance or sensitivity in barley.
2023-07-29 | GSE220532 | GEO
Project description:Gene expression analysis by high-throughtput RNA-sequencing from roots of waterlogged jatropha (Jatropha curcas). Six leaf stage seedlings (~30 d.o.) were subjected to 24 h of soil waterlogging. 4 samples, 2 conditions (24 h nonstress and 24 h waterlogging stress) and 2 independent biological replicates of 2 mRNA pools
2014-11-05 | E-GEOD-57428 | biostudies-arrayexpress
Project description:We show that an abrupt waterlogging treatment of Arabidopsis thaliana plants triggers a systemic ROS and calcium wave response, and that the waterlogging-triggered ROS wave response is dependent on RBOHD, calcium-permeable channels GLR3.3 and GLR3.6, and aquaporin PIP2;1 proteins. We further show that waterlogging stress is accompanied by a rapid systemic transcriptomic response that is evident as early as 10 min following waterlogging initiation and is partially dependent on RBOHD. Interestingly, the abrupt waterlogging stress resulted in the triggering of a rapid hydraulic wave response and the transient opening of stomata on leaves. Taken together, our findings reveal that the initiation of waterlogging stress in plants is accompanied by rapid systemic transcriptomic and physiological responses that involve the ROS, calcium, and hydraulic waves. These findings reveal that systemic plant responses to waterlogging stress are rapid and at least partially dependent on cell-to-cell signaling mechanisms.
2024-05-06 | GSE225407 | GEO
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response Plants of cotton cultivar Sicot 71 were grown to the two-leaf stage in tubs. For stress treatments plants were either watered as normal or flooded with water to completely submerge the root system. At four and twenty-four hours post-flooding samples of root or leaf tissue were taken from control and flooded plants. Total RNA was extracted from each tissue sample and assayed on cotton Affymetrix chips. Two biological replications were used for each comparison.
2010-05-17 | E-GEOD-16467 | 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 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:Waterlogging of plants leads to low oxygen levels (hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and protein synthesis. Our research seeks to characterize the gene regulatory networks associated with short-term waterlogging. MicroRNAs (miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic responses. To characterize the involvement of miRNAs in response to hypoxia conditions, a quantitative reverse transcriptase PCR (qRT-PCR) assay was used to profile the expression changes of the 22 candidate mature miRNAs, which were selected from small RNA library of waterlogging resistant line Hz32 and 84 of their predicted targets in three inbred Zea mays lines that showed different tolerance to waterlogging. Based on our studies, miR164, miR167, miR172, miR408 and miR528, which are involved in aerenchyma and root cap formation, lateral root development, root/shoot elongation and plant cell detoxification, found to be key regulator under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress-related cis-regulatory elements on the promoters of these miRNAs using the B73 reference and a miRNA-mediated gene regulatory network was constructed. The differential expression patterns of miRNAs and their targets in these three inbred lines suggest that the miRNAs are active participants in the signal transduction at the early stage of hypoxia conditions via a complex network and biochemical pathways. Our study also suggests that there might be a miRNA-mediated energy-saving strategy in surviving from waterlogging. Examination of miRNA expression in maize root under 4h waterlogging treatment
2011-10-15 | E-GEOD-32983 | biostudies-arrayexpress
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response
2009-12-18 | GSE16467 | 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