Transcriptomic and anatomic profiling reveal germination process of different wheat varieties in response to waterlogging stress
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ABSTRACT:
PROVIDER: PRJNA604012 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10990700_1.fastq.gz | Fastqsanger.gz | |||
| SRR10990700_2.fastq.gz | Fastqsanger.gz | |||
| SRR10990683_1.fastq.gz | Fastqsanger.gz | |||
| SRR10990683_2.fastq.gz | Fastqsanger.gz | |||
| SRR10990684_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Waterlogging was one of the most serious abiotic stresses in wheat-growing regions of China. There were great differences in waterlogging tolerance among different wheat varieties, and the mechanism of waterlogging tolerance of wheat seeds during germination was unclear. Methods: In order to reveal the adaptability of wheat to waterlogging stress during germination, we analyzed the germination rate and anatomical structure of three wheat seeds, ‘Zhoumai 22’, ‘Bainong 207’ and ‘Bainong 607’. At the same time, Illumina sequencing technology was used to determine the transcriptome of these three wheat varieties during germination. Results: The results showed that there was no significant difference between the germination rate of ‘Bainong 207’ after 3 days of waterlogging treatment and that of the control seeds. However, under waterlogging stress, the degree of emulsification and degradation of endosperm cells was higher than that of the control treatment, and starch granules in endosperm were significantly reduced. Transcriptome data were obtained from seed samples (a total of 18 samples) of three wheat varieties under waterlogging and control treatment. A total of 2,775 differentially expressed genes (DEGs) were identified by comprehensive analysis. In addition, by analyzing the correlation between the expression levels of DEGs and seed germination rates in three wheat varieties under waterlogging stress, it was found that the relative expression levels of 563 and 398 genes were positively and negatively correlated with the germination rate of wheat seeds, respectively. The GO and KEGG analysis found that the difference in waterlogging tolerance of the three wheat varieties was related to the abundance of key genes involved in the glycolysis pathway, the starch and sucrose metabolism pathway, and the lactose metabolism pathway. The ethanol dehydrogenase (ADH) gene in the endosperm of ‘Bainong 607’ was immediately induced after a short period of waterlogging, and the energy provided by glycolysis pathway enabled the seeds of ‘Bainong 607’ to germinate as early as possible, while the expression level of AP2/ERF transcription factor was up-regulated to further enhance its waterlogging tolerance. Conclusions: In general, this study provided a deeper understanding of the mechanisms by which different wheat varieties respond to waterlogging stress during germination.
2020-01-31 | GSE144554 | GEO
Project description:Waterlogging leads to major crop losses globally, particularly for waterlogging sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related QTLs have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging, and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA-sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called ‘core hypoxia response genes’, thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study ‘predisposition’ to waterlogging tolerance or sensitivity in barley.
2023-07-29 | GSE220532 | GEO
Project description:BackgroundWaterlogging is one of the most serious abiotic stresses affecting wheat-growing regions in China. Considerable differences in waterlogging tolerance have been found among different wheat varieties, and the mechanisms governing the waterlogging tolerance of wheat seeds during germination have not been elucidated.ResultsThe results showed no significant difference between the germination rate of 'Bainong 207' (BN207) (after 72 h of waterlogging treatment) and that of the control seeds. However, the degree of emulsification and the degradation rate of endosperm cells under waterlogging stress were higher than those obtained with the control treatment, and the number of amyloplasts in the endosperm was significantly reduced by waterlogging. Transcriptomic data were obtained from seed samples (a total of 18 samples) of three wheat varieties, 'Zhoumai 22' (ZM22), BN207 and 'Bainong 607' (BN607), subjected to the waterlogging and control treatments. A comprehensive analysis identified a total of 2775 differentially expressed genes (DEGs). In addition, an analysis of the correlations among the expression difference levels of DEGs and the seed germination rates of the three wheat varieties under waterlogging stress revealed that the relative expression levels of 563 and 398 genes were positively and negatively correlated with the germination rate of the wheat seeds, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the difference in the waterlogging tolerance among the three wheat varieties was related to the abundance of key genes involved in the glycolysis pathway, the starch and sucrose metabolism pathway, and the lactose metabolism pathway. The alcohol dehydrogenase (ADH) gene in the endosperm of BN607 was induced immediately after short-term waterlogging, and the energy provided by the glycolysis pathway enabled the BN607 seeds to germinate as early as possible; in addition, the expression of the AP2/ERF transcription factor was upregulated to further enhance the waterlogging tolerance of this cultivar.ConclusionsTaken together, the results of this study help elucidate the mechanisms through which different wheat varieties respond to waterlogging stress during germination.
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Project description:Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response
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Project description:Cuticular waxes coating leaf surfaces can help tolerate drought events by reducing non-stomatal water loss. Despite their role in drought tolerance, little is known about the cuticular wax responses of Canadian bread wheat varieties. To fill in this gap, RNAseq was performed on the flag leaf of four modern varieties to identify potential markers that could be used for selection of higher accumulation of cuticular waxes. This analysis revealed that the W1 locus is a good candidate for higher accumulation of β-diketones.
2024-08-01 | GSE254797 | GEO
Project description:Purpose: To gain a better understanding of the molecular mechanisms that enable de novo AR primordia emergence upon waterlogging, the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, Zaoer-N (waterlogging tolerant) and Pepino (waterlogging sensitive), which differed in their abilities to form AR were compared. Conclusion: This research broadens our understanding of the mechanism underlying waterlogging-triggered ARs emergence, and provides valuable information for the breeding of cucumber with enhanced waterlogging tolerance.
2022-04-29 | GSE130467 | GEO
Project description:Gene expression analysis by high-throughtput RNA-sequencing from roots of waterlogged jatropha (Jatropha curcas). Six leaf stage seedlings (~30 d.o.) were subjected to 24 h of soil waterlogging. 4 samples, 2 conditions (24 h nonstress and 24 h waterlogging stress) and 2 independent biological replicates of 2 mRNA pools
2014-11-05 | E-GEOD-57428 | biostudies-arrayexpress
Project description:We show that an abrupt waterlogging treatment of Arabidopsis thaliana plants triggers a systemic ROS and calcium wave response, and that the waterlogging-triggered ROS wave response is dependent on RBOHD, calcium-permeable channels GLR3.3 and GLR3.6, and aquaporin PIP2;1 proteins. We further show that waterlogging stress is accompanied by a rapid systemic transcriptomic response that is evident as early as 10 min following waterlogging initiation and is partially dependent on RBOHD. Interestingly, the abrupt waterlogging stress resulted in the triggering of a rapid hydraulic wave response and the transient opening of stomata on leaves. Taken together, our findings reveal that the initiation of waterlogging stress in plants is accompanied by rapid systemic transcriptomic and physiological responses that involve the ROS, calcium, and hydraulic waves. These findings reveal that systemic plant responses to waterlogging stress are rapid and at least partially dependent on cell-to-cell signaling mechanisms.
2024-05-06 | GSE225407 | GEO
Project description:Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulators are conserved in B. napus suggesting a shared regulatory network with other plants species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable, not only to evaluate germination performance of B. napus accessions, but also to identify key targets for crop improvement in this important process.
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