Ontology highlight
ABSTRACT:
PROVIDER: PRJNA657262 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12454900_1.fastq.gz | Fastqsanger.gz | |||
| SRR12454900_2.fastq.gz | Fastqsanger.gz | |||
| SRR12454901_1.fastq.gz | Fastqsanger.gz | |||
| SRR12454901_2.fastq.gz | Fastqsanger.gz | |||
| SRR12454902_1.fastq.gz | Fastqsanger.gz |
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Project description:BACKGROUND: Climate change will lead in the future to an occurrence of heat waves with a higher frequency and duration than observed today, which has the potential to cause severe damage to seedlings of temperate maize genotypes. In this study, we aimed to (I) assess phenotypic variation for heat tolerance of temperate European Flint and Dent maize inbred lines, (II) investigate the transcriptomic response of temperate maize to linearly increasing heat levels and, (III) identify genes associated with heat tolerance in a set of genotypes with contrasting heat tolerance behaviour. RESULTS: Strong phenotypic differences with respect to heat tolerance were observed between the examined maize inbred lines on a multi-trait level. We identified 607 heat responsive genes as well as 39 heat tolerance genes. CONCLUSION: Our findings indicate that individual inbred lines developed different genetic mechanisms in response to heat stress. We applied a novel statistical approach enabling the integration of multiple genotypes and stress levels in the analysis of abiotic stress expression studies.
2016-10-20 | GSE88917 | GEO
Project description:To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in maize, we generated small RNA sequences from maize seedlings that grew under control and under dought, salt, and cold stress treatments.
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Project description:Transcriptome of Zea mays genotypes under control and stress conditions. Stress conditions include heat, cold, salt, and UV. We extracted and sequenced RNA from 14 day old seedlings of inbred lines B73, Mo17 and Oh43 grown using standard conditions as well as seedlings that had been subjected to cold (5°C for 16 hours), heat (50°C for 4 hours), high salt (watered with 300 mM NaCl 20 hours prior to collection) or UV stress (2 hours). For each stress the plants were sampled immediately following the stress treatment and there were no apparent morphological changes in these plants relative to control plants.
2015-01-31 | E-MTAB-4258 | biostudies-arrayexpress
Project description:To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in maize, we generated small RNA sequences from maize seedlings that grew under control and under dought, salt, and cold stress treatments. Sequencing of small RNAs in maize under control, drought, salt, and cold stress conditions.
2015-10-21 | E-GEOD-33211 | biostudies-arrayexpress
Project description:<p>Cold stress negatively affects maize (<em>Zea mays</em> L.) growth, development and yield. Metabolic adjustments contribute to the adaptation of maize under cold stress. We show here that the transcription factor INDUCER OF CBF EXPRESSION 1 (ZmICE1) plays a prominent role in reprogramming amino acid metabolome and <em>COLD-RESPONSIVE</em> (<em>COR</em>) genes during cold stress in maize. Derivatives of amino acids glutamate/asparagine (Glu/Asn) induce a burst of mitochondrial reactive oxygen species, which suppress the cold-mediated induction of <em>DEHYDRATION RESPONSE ELEMENT-BINDING PROTEIN 1</em> (<em>ZmDREB1</em>) genes and impair cold tolerance. ZmICE1 blocks this negative regulation of cold tolerance by directly repressing the expression of the key Glu/Asn biosynthesis genes, <em>ASPARAGINE SYNTHETASEs</em>. Moreover, ZmICE1 directly regulates the expression of <em>DREB1s</em>. Natural variation at the <em>ZmICE1</em> promoter determines the binding affinity of the transcriptional activator ZmMYB39, a positive regulator of cold tolerance in maize, resulting in different degrees of <em>ZmICE1</em> transcription and cold tolerance across inbred lines. This study thus unravels a mechanism of cold tolerance in maize and provides potential targets for engineering cold-tolerant varieties.</p>
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Project description:Chilling is a major stress to plants of subtropical and tropical origins including maize. To reveal molecular mechanisms underlying chilling tolerance and chilling survival, we investigated maize transcriptome responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity for survival. Chilling stress on maize shoots and roots is found to each contribute to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacity reveals that chilling survival in maize is highly associated with upregulation in leaves and crowns of abscisic acid response pathway, transcriptional regulators and cold response as well as downregulation of heat response in crowns. Comparison of chilling treatment on whole and part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental perception. In sum, this study details chilling responses in leaves, roots and crowns and reveals potential chilling survival mechanism in maize, which lays ground for further understanding survival and tolerance mechanisms under low but non-freezing temperatures in tropical and subtropical plants.
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Project description:Studies investigating crop resistance to biotic and abiotic stress have largely focused on plant responses to singular forms of stress and individual biochemical pathways that only partially represent stress responses. Thus, combined biotic and abiotic stress treatments and the global assessment of their elicited metabolic expression remains largely unexplored. In this study, we employed targeted and untargeted metabolomics to investigate the metabolic responses of maize (Zea mays) to both individual and combinatorial stress treatments using heat (abiotic) and Cochliobolus heterostrophus infection (biotic) experiments. Ultra-high-performance liquid chromatography-high-resolution mass spectrometry revealed significant metabolic responses to C. heterostrophus infection and heat stress, and comparative analyses between these individual forms of stress demonstrated differential elicitation between the two global metabolomes. In combinatorial experiments, treatment with heat stress prior to fungal inoculation negatively impacted maize disease resistance against C. heterostrophus, and distinct metabolome separation between combinatorial stressed plants and the non-heat stressed infected controls was observed. Targeted analysis revealed inducible primary and secondary metabolite responses to biotic/abiotic stress, and combinatorial experiments indicated that deficiency in the hydroxycinnamic acid, p-coumaric acid, may lead to the heat-induced susceptibility of maize to C. heterostrophus. Collectively, these findings demonstrate that abiotic stress can predispose crops to more severe disease symptoms, underlining the increasing need to investigate defense chemistry in plants under combinatorial stress.
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Project description:DNA methylation is a chromatin modification that is sometimes associated with epigenetic regulation of gene expression. As DNA methylation can be reversible at some loci, it is possible that methylation patterns may change within an organism that is subjected to environmental stress. In order to assess the effects of abiotic stress on DNA methylation patterns in maize (Zea mays), we subjected seedlings to heat, cold and UV stress treatments. Tissue was later collected from individual adult plants that had been subjected to stress or control treatments and used to perform DNA methylation profiling to determine whether there were consistent changes in DNA methylation triggered by specific stress treatments. The DNA methylation profiling was performed by immunoprecipitation of methylated DNA followed by microarray hybridization to allow for quantitative estimates of DNA methylation abundance throughout the low-copy portion of the maize genome. By comparing the DNA methylation profiles of each individual plant to the average of the control plants it was possible to identify regions of the genome with variable DNA methylation. However, we did not find evidence of consistent DNA methylation changes resulting from the stress treatments used in this study. Instead, the data suggest that there is a low-rate of stochastic variation that is present in both control and stressed plants. Methylation profiles in flag leaf tissue of maize inbred lines under various stress conditions using a custom 1.4M feature NimbleGen array. Methylation profiles of flag leaf tissue from 18 B73 inbred lines that underwent various stresses as seedlings. This includes 5 cold treatment plants, 4 UV treated plants, 3 heat treated plants, and 6 total control plants (no stress). All methylation profiling was done on a custon 3x1.4M NimbleGen array platform (meDIP-chip).
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