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PROVIDER: PRJNA1229093 | ENA |
REPOSITORIES: ENA
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Project description:We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta.
2014-03-01 | GSE53995 | GEO
Project description:We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta. Examination of three root types of maize under salt treatment for understanding the different responding mechenism to salt stress.
2014-03-01 | E-GEOD-53995 | biostudies-arrayexpress
Project description:To acknowledge the molecular mechanisms underlying maize salt tolerance, two maize inbred lines, including salt-tolerant 8723 and salt-sensitive P138, were used in this study. Comparative proteomics of seedling roots from two maize inbred lines under 180 mM salt stress for 10 days was performed by the isobaric tags for relative and absolute quantitation (iTRAQ) approach. We obtained a total of 336237 spectra. 30616 peptides and a total of 7505 proteins were identified with 1% FDR. A total of 7505 differentially expressed proteins (DEPs) were identified. 626 DEPs were identified in line 8723 under salt stress, among them, 378 up-regulated and 248 down-regulated. 473 DEPs were identified in P138, of which 212 were up-regulated and 261 were down-regulated. Venn diagram analysis showed that 17 DEPs were up-regulated and 12 DEPs were down-regulated in the two inbred lines. In addition, 8 DEPs were up-regulated in line 8723 but down-regulated in P138, 6 DEPs were down-regulated in line 8723 but up-regulated in P138. In salt-stressed 8723, the DEPs were primarily associated with phenylpropanoid biosynthesis, starch and sucrose metabolism, and the MAPK signaling pathway. Intriguingly, the DEPs were only associated with the nitrogen metabolism pathway in P138. Compared to P138, the root response to salt stress in 8723 could maintain stronger water retention capacity, osmotic regulation ability, synergistic effects of antioxidant enzymes, energy supply capacity, signal transduction, ammonia detoxification ability, lipid metabolism, and nucleic acid synthesis. Based on the proteome sequencing information, changes in the abundance of 8 DEPs were correlated with the corresponding mRNA levels. Our results from this study may elucidate some details of salt tolerance mechanisms and salt tolerance breeding of maize.
2019-11-12 | PXD014409 | Pride
Project description:Salt stress is one major abiotic stress limiting maize grain yield throughout the world.To better understand maize salt tolerance molecular mechanism, comparative proteomic analysis was conducted on seedling roots of salt-tolerant genotype Jing724 and salt-sensitive genotype D9H under NaCl. Jing724 exhibited significantly higher germination rate and growth parameters (weight/length) than did D9H under salt treatment.We identified 565 differentially regulated proteins (DRP) using iTRAQ and 89 were specific to Jing724 while 424 were specific to D9H. In salt stressed Jing724, pentose phosphate pathway, glutathione metabolism and nitrogen metabolism were enriched. By pathway enrichment and protein-protein interaction analyses, key DRPs such as glucose-6-phosphate 1-dehydrogenase, NADPH producing dehydrogenase, glutamate synthase and glutamine synthasewere identified.Additionally, salt responsive proteins of Jing724 were indicated to facilitate energy management, maintenance of redox homeostasis, reducing ammonia toxicity, osmotic homeostasis regulation, stress defense, stress adaptation, biotic cross-tolerance and gene transcription regulation. Quantification of multiple metabolic or enzymatic changes including SOD activity, MDA content, relative electrolyte leakage and Proline content were consistent with their predicted changes based on functions of DRPs. DRP analysis was correlated with the mRNA transcripts abundancevariation of eight representative DRPs. These results contribute to elucidating molecular networks of salt tolerance.
2017-12-05 | PXD007802 | Pride
Project description:Salt stress is one major abiotic stress limiting maize grain yield throughout the world.To better understand maize salt tolerance molecular mechanism, comparative proteomic analysis was conducted on seedling roots of salt-tolerant genotype Jing724 and salt-sensitive genotype D9H under NaCl. Jing724 exhibited significantly higher germination rate and growth parameters (weight/length) than did D9H under salt treatment.We identified 565 differentially regulated proteins (DRP) usingiTRAQ and 89 were specific to Jing724 while 424 were specific to D9H. In salt stressed Jing724, pentose phosphate pathway, glutathione metabolism and nitrogen metabolism were enriched. By pathway enrichment and protein-protein interaction analyses, key DRPs such as glucose-6-phosphate 1-dehydrogenase, NADPH producing dehydrogenase, glutamate synthase and glutamine synthasewere identified.Additionally, salt responsive proteins of Jing724 were indicated to facilitate energy management, maintenance of redox homeostasis, reducing ammonia toxicity, osmotic homeostasis regulation, stress defense, stress adaptation, biotic cross-tolerance and gene transcription regulation. Quantification of multiple metabolic or enzymatic changes including SOD activity, MDA content, relative electrolyte leakage and Proline content were consistent with their predicted changes based on functions of DRPs. DRP analysis was correlated with the mRNA transcripts abundance variation of eight representative DRPs. These results contribute to elucidating molecular networks of salt tolerance.
2017-12-05 | PXD007711 | Pride
Project description:Although previous studies have addressed the possible benefits of arbuscular mycorrhizal (AM) symbiosis for rice plants under salinity, the underlying molecular mechanisms are still unclear. Here, we showed that rice colonized with AM fungi had better growth performance and higher K+/Na+ ratio under salt stress. Differentially expressed genes (DEGs) responding to AM symbiosis especially under salt stress were obtained from RNA sequencing. AM-regulated DEGs in cell wall modification and peroxidases categories were mainly upregulated in shoots, suggesting AM symbiosis might assist in relaxing the cell wall and scavenging reactive oxygen species (ROS). AM symbiosis indeed improved ROS scavenging capacity in rice shoots under salt stress. In addition, genes involved in Calvin cycle and terpenoid synthesis were enhanced by AM symbiosis in shoots and roots under salt stress, respectively. AM-upregulated cation transporters and aquaporin in both shoots and roots were highlighted. Strikingly, “protein tyrosine kinase activity” subcategory was the most significantly over-represented GO term among all AM-upregulated and downregulated DEGs in both shoots and roots, highlighting the importance of kinase on AM-enhanced salinity tolerance. Overall, our results from the transcriptomic analyses indicate that AM symbiosis uses a multipronged approach to help plants achieve salt stress tolerance.
2022-04-18 | GSE200863 | GEO
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:Salinization poses a significant challenge in agriculture, exacerbated by anthropogenic global warming. Biostimulants, derived from living microorganisms or natural extracts, have emerged as valuable tools for conventional and organic agriculture. However, our understanding of the molecular mechanisms underlying the effects of biostimulants is very limited, especially in crops under real cultivation conditions. In this study, we adopted an integrative approach to investigate the effectiveness of the combined application of plant growth-promoting bacterium (Bacillus megaterium strain BM08) and a non-microbial biostimulant under control conditions (normal watering) and salt stress. After confirming the yield increase under both conditions, we investigated the molecular mechanisms underlying the observed effect by measuring a number of physiological parameters (i.e., lipid peroxidation, antioxidants, chlorophylls, total phenolics and phytohormone content), as well as RNA sequencing and primary metabolite analyses. Our findings reveal that the combined effect of the microbial and non-microbial biostimulants led to a decrease in the antioxidant response and an up-regulation of genes involved in cytokinin biosynthesis under salt stress conditions. This, in turn, resulted in a higher concentration of the bioactive cytokinin, isopentenyladenosine, in roots and leaves and an increase in γ-aminobutyric acid, a non-proteic amino acid related to abiotic stress responses. In addition, we observed a decrease in malic acid, along with an abscisic acid (ABA)-independent up-regulation of SR-kinases, a family of protein kinases associated with abiotic stress responses. Furthermore, we observed that the single application of the non-microbial biostimulant triggers an ABA-dependent response under salt stress; however, when combined with the microbial biostimulant, it potentiated the mechanisms triggered by the BM08 bacterial strain. This comprehensive investigation shows that the combination of two biostimulants is able to elicit a cytokinin-dependent response that may explain the observed yield increase under salt stress conditions.
2024-10-15 | GSE279211 | GEO