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PROVIDER: PRJNA916486 | ENA |
REPOSITORIES: ENA
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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:High temperature is increasingly becoming one of the prominent environmental factors affecting the growth and development of maize (Zea mays L.). Therefore, it is critical to identify key genes and pathways related to heat stress (HS) tolerance in maize. Here, we identified a heat-resistant (Z58D) and heat-sensitive (AF171) maize inbred lines at seedling stage. Transcriptomic analysis identified 3,006 differentially expressed genes (DEGs) in AF171 and 4,273 DEGs in Z58D under HS treatments, respectively. Subsequently, GO enrichment analysis showed that shared upregulated genes in AF171 and Z58D involved in response to HS, protein folding, abiotic and temperature stimulus pathway. Moreover, the comparison between the two inbred lines under HS showed that response to heat and response to temperature stimulus significantly overrepresented for the 1,234 upregulated genes. Furthermore, commonly upregulated genes in Z58D and AF171 had higher expression level in Z58D than AF171. In addition, maize inbred CIMBL55 had been verified to be more tolerant than B73 and commonly upregulated genes had higher expression level in CIMBL55 than B73 under HS. The consistent results indicated that heat-resistant inbred lines may coordinate the remarkable expression of genes in order to recover from HS. Additionally, 35 DEGs were conserved among 5 inbred lines by a comparative transcriptomic analysis. Most of them were more pronounced in Z58D than AF171 at expression level. Those candidate genes may confer thermotolerance in maize.
2024-03-01 | GSE254852 | GEO
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.
2020-08-03 | ST001489 | MetabolomicsWorkbench
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).
2016-01-07 | E-GEOD-65266 | biostudies-arrayexpress
Project description:Maize is a staple food, feed, and industrial crop. Heat stress (HS) is one of the major stresses affecting maize production and is usually accompanied by other stresses, such as drought. Our previous study identified a heterotrimer complex, ZmNF-YA1-YB16-YC17, in maize. ZmNF-YA1 and ZmNF-YB16 were positive regulators of the drought stress response and were involved in maize root development. In this study, we investigated whether ZmNF-YA1 confers HS tolerance in maize. The ZmNF-YA1 mutant and overexpression lines were used to test the role of ZmNF-YA1 in maize thermotolerance. The ZmNF-YA1 mutant was more temperature-sensitive than the WT, while the ZmNF-YA1 overexpression lines showed a thermotolerant phenotype. Higher malondialdehyde content and reactive oxygen species accumulation were observed in the mutant, followed by WT and overexpression lines after HS treatment, while an opposite trend was observed for chlorophyll content. RNA-seq was used to analyze transcriptome changes in W22 and nf-ya1 plants in response to HS at great depths. Based on their expression profiles, the HS response-related differentially expressed genes in nf-ya1 and W22 were grouped into seven clusters via k-means clustering. Gene Ontology (GO) enrichment analysis of Clade 1, in which ZmNF-YA1 and HS induced, GO terms for protein refolding and protein stabilization, and terms for various stress responses were considerably enriched. Thus, the contribution of ZmNF-YA1 to protein stabilization, refolding, and regulation of ABA, ROS, and heat/temperature signaling may be the major reason why ZmNF-YA1 overexpression enhanced heat tolerance, and the mutant showed a heat-sensitive phenotype.
2024-06-02 | GSE268429 | GEO
Project description:Methylation of chromosomal DNA in animals and plants is a fundamental mechanism of epigenetic regulation, and the maize genome, with its diverse complement of transposons and repeats, is a paradigm for transgenerational mechanisms such as paramutation and imprinting. We have determined the genome-wide cytosine methylation map of two maize inbred lines, B73 and Mo17, at high coverage and at single nucleotide resolution. Transposon methylation is highest in CG (65%) and CHG (50%) contexts (where H = A, C or T), while methylation in CHH (5%) contexts is guided by 24nt small interfering RNA (siRNA), and not by 21-22nt siRNA. We have found that CG (8%) methylation seems to deter insertion of Mutator transposons into exons, while CHH and CHG methylation at splice donor and acceptor sites strongly inhibits RNA splicing. Methylation differences between parents are inherited in recombinant inbred lines, but methylation switches, guided by siRNA, are widespread and persist for up to 8 generations. These differences influence splicing, and recurrent switching suggest that paramutation is much more common than previously supposed, and may contribute to heterosis. Our results provide a comprehensive high resolution resource for maize genome methylation, as well as a map of recurrent transgenerational epigenetic shifts (paramutation) in the two most commonly used inbred maize lines. Genome-wide cytosine methylation map in 2 maize strains by bisulfite sequencing, and RNA and small RNA profiles in the same tissue using Illumina platform.
2013-06-03 | E-GEOD-39232 | biostudies-arrayexpress
Project description:An understanding of how genetic variants affect chromatin accessibility in unique cellular context remains poorly understood. Here, we generated single-cell chromatin accessibility profiles in nearly 200 diverse maize inbred lines, revealing for the first time variants that affect chromatin accessibility in distinct cellular contexts.
2024-11-19 | GSE275409 | GEO
Project description:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. At present there is relatively little information regarding the role of miRNAs in the response to drought stress in maize. In this study, two small RNA libraries were sequenced, and a total of 11,973,711 and 14,326,010 raw sequences were generated from growing leaves of drought-tolerant and drought-sensitive maize seedlings, respectively. Further analysis identified 192 mature miRNAs, which include 124 known maize (zma) miRNAs and 68 potential novel miRNA candidates. Additionally, 167 target genes (259 transcripts) of known and novel miRNAs were predicted to be differentially expressed between two maize inbred lines. Of these, three novel miRNAs were up-regulated and two were down-regulated under drought stress. The expression of these five miRNAs and nine target genes was confirmed using quantitative reverse transcription PCR. The expression of three of the miRNAs and their putative target genes exhibited an inverse correlation, and expression analysis suggested that all five may play important roles in maize leaves. Finally, GO annotations of the target genes indicated a potential role in photosynthesis, may therefore contribute to the drought stress response. This study describes the identification and characterization of novel miRNAs that are the differentially expressed in drought-tolerant and drought-sensitive inbred maize lines. This provides the foundation for further investigation into the mechanism of miRNA function in response to drought stress in maize.
2015-06-01 | GSE61700 | GEO
Project description:Here, in order to study maize drought stress responses at the molecular level, we have employed omics strategy to perform transcriptome and proteome profiling of drought contrasting maize lines at the various stages. We conducted a comparative analysis of different maize varieties at various stages after drought treatment. In addition, we evaluated some physiological responses of these maize lines under drought stress, and the results of this study provide further insights into the drought stress tolerance signatures in maize.
2019-09-23 | PXD015533 |
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