Identification of circular RNAs and their targets in leaves of Triticum aestivum L. under dehydration stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Triticum aestivum
PROVIDER: GSE86641 | GEO | 2017/03/08
SECONDARY ACCESSION(S): PRJNA342474
REPOSITORIES: GEO
Similar Datasets
Project description:Circular RNAs (circRNAs) are a type of newly identified non-coding RNAs through high-throughput deep sequencing, which play important roles in miRNA function and transcriptional controlling in human, animals, and plants. To date, there is no report in wheat seedlings regarding the circRNAs identification and roles in the dehydration stress response. In present study, the total RNA was extracted from leaves of wheat seedlings under dehydration-stressed and well-watered conditions, respectively. Then, the circRNAs enriched library based deep sequencing was performed and the circRNAs were identified using bioinformatics tools. Around 88 circRNAs candidates were isolated in wheat seedlings leaves while 62 were differentially expressed in dehydration-stressed seedlings compared to well-watered control. Among the dehydration responsive circRNAs, six were found to act as 26 corresponding miRNAs sponges in wheat. Sixteen circRNAs including the 6 miRNAs sponges and other 10 randomly selected ones were further validated to be circular by real-time PCR assay, and 14 displayed consistent regulation patterns with the transcriptome sequencing results. After Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the targeted mRNAs functions, the circRNAs were predicted to be involved in dehydration responsive process, such as photosynthesis, porphyrin, and chlorophyll metabolism, oxidative phosphorylation, amino acid biosynthesis, and metabolism, as well as plant hormone signal transduction, involving auxin, brassinosteroid, and salicylic acid. Herein, we revealed a possible connection between the regulations of circRNAs with the expressions of functional genes in wheat leaves associated with dehydration resistance.
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Project description:MicroRNAs (miRNAs) play critical roles in the processes of plant growth and development, but little is known of their functions during dehydration stress in wheat. Moreover, the mechanisms by which miRNAs confer different levels of dehydration stress tolerance in different wheat genotypes are unclear.We examined miRNA expressions in two different wheat genotypes, Hanxuan10, which is drought-tolerant, and Zhengyin1, which is drought-susceptible. Using a deep-sequencing method, we identified 367 differentially expressed miRNAs (including 46 conserved miRNAs and 321 novel miRNAs) and compared their expression levels in the two genotypes. Among them, 233 miRNAs were upregulated and 10 were downregulated in both wheat genotypes after dehydration stress. Interestingly, 13 miRNAs exhibited opposite patterns of expression in the two wheat genotypes, downregulation in the drought-tolerant cultivar and upregulation in the drought-susceptible cultivar. We also identified 111 miRNAs that were expressed predominantly in only one or the other genotype after dehydration stress. We verified the expression patterns of a number of representative miRNAs using qPCR analysis and northern blot, which produced results consistent with those of the deep-sequencing method. Moreover, monitoring the expression levels of 10 target genes by qPCR analysis revealed negative correlations with the levels of their corresponding miRNAs.These results indicate that differentially expressed patterns of miRNAs between these two genotypes may play important roles in dehydration stress tolerance in wheat and may be a key factor in determining the levels of stress tolerance in different wheat genotypes.
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Project description:Ascorbate-glutathione (ASA-GSH) cycle is a major pathway of H2O2 scavenging and an effective mechanism of detoxification in plants. The differences in photosynthesis, chlorophyll content (Chl), relative water content (RWC), antioxidants and antioxidative enzyme activities involved in ASA-GSH metabolism were measured between the flag leaves and spike bracts (glumes and lemmas) during grain filling under drought stress. The expression of APX1, GRC1, DHAR, MDHAR, GPX1, and GS3 in ASA-GSH cycle was also measured. Compared with the flag leaves, the spike bracts exhibited stable net photosynthetic rate (PN) and chlorophyll content (Chl), a lower accumulation of reactive oxygen species (ROS), and more enhanced percentages of antioxidant enzyme activities and key enzymes gene transcription levels involved in ASA-GSH metabolism during the grain-filling stage under drought conditions. This could be the reasonable explanation for the more stable photosynthetic capacity in spikes, and the glumes and lemmas senesced later than the flag leaves at the late grain-filling stage. Also, the function of ASA-GSH cycle could not be ignored in alleviating oxidative damage by scavenging more excess ROS in spikes under drought stress.
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Project description:Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. circRNAs were extraordinarily enriched in the mammalian brain, well conserved in sequence, often expressed as circRNAs in both human and mouse, and sometimes even detected in Drosophila brains. circRNAs were overall upregulated during neuronal differentiation, highly enriched in synapses, and often differentially expressed compared to their mRNA isoforms. circRNA expression correlated negatively with expression of the RNA-editing enzyme ADAR1. Knockdown of ADAR1 induced elevated circRNA expression. Together, we provide a circRNA brain expression atlas and evidence for important circRNA functions and values as biomarkers. To assess circRNA expression in mammalian brain, we sequenced and analyzed mouse brain regions (hippocampus, cerebellum, prefrontal cortex and olfactory bulb), various neuronal differentiation (mouse P19 and human SH-SY5Y cells) and maturation (mouse cortical neurons) stages, and subcellular compartments in mouse (synaptoneurosomal fraction, cytoplasmic fraction, whole brain lysate).
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Project description:Fructans represent the major component of water soluble carbohydrates (WSCs) in the maturing stem of temperate cereals and are an important temporary carbon reserve for grain filling. Theoretically, genotypic variation in carbon reserve accumulation is determined by relative carbon availability and demand at the whole plant level. To evaluate the importance of source carbon availability in fructan accumulation and its associated molecular mechanisms, we performed comparative analyses of individual WSC components and the expression profiles of genes involved in major carbohydrate metabolism and photosynthesis in flag leaves of recombinant inbred lines derived from a cross between wheat cultivars Seri M82 and Babax (SB lines). High sucrose levels in the mature flag leaf (source carbon organ) were found to be positively associated with WSC and fructan concentrations in both the leaf and stem of SB lines in several field trials. Analysis of Affymetrix expression array data revealed that high leaf sucrose lines grown in abiotic-stress-prone environments had high expression levels of a number of genes in the leaf involved in the sucrose synthetic pathway and photosynthesis, such as Calvin cycle genes, antioxidant genes involved in the removal of chloroplast H2O2 and genes involved in energy dissipation. The expression of the majority of genes involved in fructan and starch synthetic pathways were positively correlated with sucrose levels in the leaves of these SB lines.
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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Triticum aestivum tissues (including leaves and spiklets infected with Fusarium and control). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.
2011-09-30 | GSE32476 | GEO
Project description:Plant roots are inhabited by an enormous variety of microorganisms, including fungi, which can control the growth as well as regulate the health of the host plants. The mycobiome composition of the roots of wheat plants, especially spelt, under drought stress has been rarely investigated. Therefore, the aim of the present study was to examine the composition of fungal communities in the root endosphere and rhizosphere of three Triticum aestivum ssp. spelta L. cultivars and one Triticum aestivum ssp. vulgare L. cultivar, grown under drought and controlled conditions in different soil preparations. Culture-dependent fungal community profiling was performed to examine the impact of rhizocompartments (endosphere, rhizosphere), host genotype, watering status and different soil preparation on roots mycobiome structure. A total of 117 fungal strains, belonging to 22 genera, were found to colonize the internal and external parts of roots in T. aestivum ssp. spelta L. and T. aestivum ssp. vulgare L. cultivars. The results showed that the part of root and soil preparation type significantly determined the mycobiome composition of wheat roots.
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Project description:Background: The Faradarmani Consciousness Field was founded by Mohammad Ali Taheri. It is a novel field and is described similarly to the field of gravity, or the electromagnetic field. This field is neither matter nor energy, and therefore does not possess a quantity. Even though there is no direct scientific evidence for the Consciousness Field, it is possible to investigate its effects on objects through controlled experiments. The aim of the present work was to study the alleviative effects of the Faradarmani Consciousness Field on common wheat Triticum aestivum L. var Star under salt stress. Methods: Plants were grown under 0 mM NaCl (control) and 150 mM NaCl with or without the influence of Faradarmani Consciousness Field for 3 weeks. Chlorophyll, hydrogen peroxide (H 2O 2), malondialdehyde (MDA) content and activity of antioxidant enzymes such as superoxide dismutase (SOD),polyphenol oxidase (PPO), and peroxidase (POX) were measured in all groups of plants. Results: In the salt-treated plants under the influence of the Faradarmani Consciousness Field, the contents of total chlorophyll, as well as a and b chlorophyll forms, were elevated compared with the salt-treated plants without Faradarmani CF (34.8%, 17.8%, and 169% respectively). Additionally, Faradarmani increased H 2O 2 (57%) and the activity of SOD and PPO by 220% and 168%, respectively, under salinity compared with the salt-treated plants without Faradarmani CF. MDA content and activity of peroxidase were decreased by 12.5% and 34%, respectively. Conclusion: These results suggest the Faradarmani Consciousness Field as a qualitative intervention strategy to withstand salt stress in plants, by increasing the contents of chlorophyll, antioxidant enzyme activities, and decreasing MDA content under salinity.
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Project description:Globally from abiotic stresses, salt stress is the major stress that limits crop production. One of them is wheat that has been utilized by more than 1/3 of the world population as staple food due to its nutritive value. Biochar is an activated carbon that can ameliorate the negative impacts on plants under saline conditions. The present study was conducted to examine the ameliorative impact of "Biochar application" to Triticum aestivum L. plant grown under salinity stress and evaluated on the basis of various growth, yield, physiological, biochemical attributes. Preliminary experiment was done to select the Triticum aestivum L. varieties with 90% germination rate for further experiment. The selected varieties, FSD08 and PUNJAB-11 of wheat were treated with two levels of sodium chloride (0 mM and 120 mM). Two varieties of wheat included FSD08 and PUNJAB-11 were treated with two levels of sodium chloride (0 mM and 120 mM). To address the impact of salt stress two levels of biochar 0% and 5% was used as exogenous application. A three way completely randomized experimentation was done in 24 pots of two wheat varieties with three replicates. The results demonstrated that salt stress affected growth, physiological attributes, yield and inorganic mineral ions (Ca2+ and K+) in roots and shoots parameters of wheat negatively while biochar overall improved the performance of plant. SOD, CAT, APX and POD activities enhanced during salt stress as the plant self-defense mechanism against salinity to minimize the damaging effect. Salt stress also significantly increased the membrane permeability, and levels of H2O2, MDA, Cl and Na ions. Biochar treatment nullified negative impacts of NaCl and improved the plant growth and yield significantly. Hence, biochar amendment can be suggested as suitable supplement for sustainable crop production under salinization.
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