Ontology highlight
ABSTRACT:
PROVIDER: PRJNA989423 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25209502_1.fastq.gz | Fastqsanger.gz | |||
| SRR25209502_2.fastq.gz | Fastqsanger.gz | |||
| SRR25209503_1.fastq.gz | Fastqsanger.gz | |||
| SRR25209503_2.fastq.gz | Fastqsanger.gz | |||
| SRR25209504_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.
2019-07-22 | GSE133573 | GEO
Project description:Melatonin is a well-known agent that plays multiple roles in animals. Its possible function in plants is less clear. In the present study, we tested the effect of melatonin (N-acetyl-5-methoxytryptamine) on soybean growth and development. Both spraying of leaves and seed-coating with melatonin significantly promoted soybean growth as judged from leaf size and plant height. This enhancement was also observed in soybean production and their fatty acid content. Melatonin increased pod number, seed number and seed weight. However, the 100-seed weight was not influenced by melatonin application. Melatonin also improved soybean tolerance to salt and drought stresses. Transcriptome analysis revealed that melatonin up-regulated the expression of many genes and alleviated the inhibitory effects of salt stress on gene expressions. Further detailed analysis of the affected pathways documents that melatonin likely achieved its promotional roles in soybean through enhancement of genes involved in cell division, photosynthesis, carbohydrate metabolism, fatty acid biosynthesis and ascorbate metabolism. Our results demonstrate that melatonin has significant potential for improving of soybean growth and seed production. Further study should uncover more about the molecular mechanisms of melatoninM-bM-^@M-^Ys function in soybeans and other crops. Four different treatments were chosen, water, salt, 100M-BM-5M melatonin and salt plus 100M-BM-5M melatonin. The comparison of salt/melatonin-treated sample versus water-treated sample reveals salt or melatonin induced transcriptome changes. The comparison of melatonin plus salt treated sample versus salt-treated sample reveals melatonin induced changes when salt exists.
2014-08-31 | E-GEOD-57960 | biostudies-arrayexpress
Project description:To explore the adaptive mechanisms of soybean in lipid signalling and remodelling of metabolism following salt stress, lipid profiling was performed on leaves of seedlings from cultivar C08 which is a salt-sensitive variety. In our previous study, C08 seedlings showed leaf drooping at 0.5 h under high salt stress followed by recovery. To study if this phenomenon could be closely linked to the dynamic changes in membrane lipid composition, integrated proteomic and lipidomic analyses were conducted. To address protein function in response to salt, label-free quantitative (LFQ) proteomic analysis on salt-treated soybean seedling leaves was conducted. Our study identified putative enzymes or protein components involved in lipid regulation and provides a comprehensive understanding of lipid remodelling following salt treatment in soybean.
2021-02-25 | PXD023092 | Pride
Project description:Salinity is one of the serious environmental constraints stresses limiting crop plants growth and yield. We have previously reported that GsCBRLK functions as a positive regulator of plant tolerance to salt stress. In order to investigate the physiological and molecular mechanisms underlying the salinity tolerance regulated by GsCBRLK, the gene was overexpressed in soybean plants. Here we examined the salt-responsive proteomes of the GsCBRLK overexpression soybean and wild typeWT plants using iTRAQ-based proteomic approach to elucidate investigate the global effects and potentialssible downstream targets of GsCBRLK protein. A total of 941 proteins showed significant changes in protein abundance in soybean leaves, and 574 of the NaCl-regulated proteins were GsCBRLK-dependent. Among the identified proteins, four protein changes in both the two genotypes after NaCl treatment were validated using Western blot analysis. The iIdentification of the salt-reponsive proteins has revealed the involvement of GsCBRLK protein in the enhancement of ROS scavenging and photosynthesis capacity in soybean plants, which was corrobarated with the physiological effects of GsCBRLK overexpression. More importantly, the proteomic data has suggested the regulatory function of GsCBRLK in salt signal transduction pathway mediated by Ca2+/CaM. These findings have contributed to our knowledge of plant GsCBRLK mediated salt tolerance mechanisms mediated by GsCBRLK.
2016-05-23 | PXD002851 | Pride
Project description:Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.
2019-07-22 | GSE133574 | GEO
Project description:This study aims at addressing soybean seeds (variety Absolute RR) germination, at 48h, during optimal and salt stressed condition when treated with bacterial signal compounds lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17). Soybean growth is negatively affected when exposed to 40 mM NaCl and exposure to 80 mM NaCl is often lethal. When treated with the bacterial signal compounds lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17), soybean seeds (variety Absolute RR) responded positively at salt stress of up to 150 mM NaCl. Shotgun proteomics of unstressed and 100 mM NaCl stressed seeds (48 h) in combination with the LCO and Th17 revealed many known, predicted, hypothetical and unknown proteins. In all, carbon, nitrogen and energy metabolic pathways were affected under both unstressed and salt stressed conditions when treated with signals. PEP carboxylase, Rubisco oxygenase large subunit, pyruvate kinase, and isocitrate lyase were some of the noteworthy proteins enhanced by the signals, along with antioxidant glutathione-S-transferase and other stress related proteins. These findings suggest that the germinating seeds alter their proteome based on bacterial signals and on stress, the specificity of this response plays a crucial role in organ maturation and transition from one stage to another in the plants life cycle; understanding this response is of fundamental importance in agriculture and, as a result, global food security.
2016-09-12 | PXD004106 | Pride
Project description:This model is from the article:
Reduction of off-flavor generation in soybean homogenates: a mathematical model.
Mellor N , Bligh F , Chandler I , Hodgman C
J. Food Sci.2010 Sep; 75(7): R131-8; PMID: 2153556,
Abstract:
The generation of off-flavors in soybean homogenates such as n-hexanal via the lipoxygenase (LOX) pathway can be a problem in the processed food industry. Previous studies have examined the effect of using soybean varieties missing one or more of the 3 LOX isozymes on n-hexanal generation. A dynamic mathematical model of the soybean LOX pathway using ordinary differential equations was constructed using parameters estimated from existing data with the aim of predicting how n-hexanal generation could be reduced. Time-course simulations of LOX-null beans were run and compared with experimental results. Model L(2), L(3), and L(12) beans were within the range relative to the wild type found experimentally, with L(13) and L(23) beans close to the experimental range. Model L(1) beans produced much more n-hexanal relative to the wild type than those in experiments. Sensitivity analysis indicates that reducing the estimated K(m) parameter for LOX isozyme 3 (L-3) would improve the fit between model predictions and experimental results found in the literature. The model also predicts that increasing L-3 or reducing L-2 levels within beans may reduce n-hexanal generation. PRACTICAL APPLICATION: This work describes the use of mathematics to attempt to quantify the enzyme-catalyzed conversions of compounds in soybean homogenates into undesirable flavors, primarily from the compound n-hexanal. The effect of different soybean genotypes and enzyme kinetic constants was also studied, leading to recommendations on which combinations might minimize off-flavor levels and what further work might be carried out to substantiate these conclusions.
2024-09-02 | BIOMD0000000415 | BioModels
Project description:Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. Results In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. Conclusions We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.
2014-11-01 | GSE57252 | GEO