Ontology highlight
ABSTRACT:
PROVIDER: PRJNA705011 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13787016_1.fastq.gz | Fastqsanger.gz | |||
| SRR13787016_2.fastq.gz | Fastqsanger.gz | |||
| SRR13787017_1.fastq.gz | Fastqsanger.gz | |||
| SRR13787017_2.fastq.gz | Fastqsanger.gz | |||
| SRR13787018_1.fastq.gz | Fastqsanger.gz |
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Project description:Wheat seed germination is highly related to seedling survival rate and subsequent vegetative growth,and therefore directly affects the conformation of wheat yield and quality. So wheat seed germination is not only important to itself, but the whole human society. However, due to the large genome size, many studies related to wheat seed are very complex and uncompleted. Transcriptome analysis of elite Chinese bread wheat cultivar Jimai 20 may provides a comprehensive understanding of wheat seed germination. Seed germination involves in the regulation of large number of genes, whether these genes are normal activated or not is very important to seed germination. We performed microarray analysis using the Affymetrix Gene Chip to reveal the gene expression profiles in five phases of wheat cultivar Jimai 20 seed germination. Our results provide a new insights into the thoroughly metabolic changes of seed germination as well as the relationship between some significant genes.
2013-08-14 | GSE49821 | GEO
Project description:Wheat seed germination directly affects wheat yield and quality. The wheat grains mainly include embryo and endosperm, and both play important roles in seed germination, seedling survival and subsequent vegetative growth. ABA can positively regulate dormancy induction and then negatively regulates seed germination at low concentrations. H2O2 treatment with low concentration can promote seed germination of cereal plants. Although various transcriptomics and proteomics approaches have been used to investigate the seed germination mechanisms and response to various abiotic stresses in different plant species, an integrative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses has not reported so far. We used the elite Chinese bread wheat cultivar Zhenmai 9023 as material and performed the first comparative transcriptome microarray analysis between embryo and endosperm response to ABA and H2O2 treatments during seed germination using the GeneChip® Wheat Genome Array Wheat seed germination includes a great amount of regulated genes which belong to many functional groups. ABA/H2O2 can repress/promote seed germination through coordinated regulating related genes expression. Our results provide new insights into the transcriptional regulation mechanisms of embryo and endosperm response to ABA and H2O2 treatments during seed germination
2014-12-11 | GSE64030 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
2022-12-01 | GSE209640 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
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Project description:sRNA-seq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.
2017-08-15 | GSE94458 | GEO
Project description:Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.
2023-11-09 | GSE234833 | GEO
Project description:How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. For the genes that are quantitatively regulated at the four stages, two antagonistic epigenetic marks, H3K4me3 and H3K27me3, together with the binding of RNA polymerase II, were investigated at the four stages by chromatin immunoprecipitation (ChIP). For 10 out of 16 genes examined, the relative enrichment of histone modification marks (H3K4me3 and H3K27me3) and RNA polymerase II binding on their promoter regions correlates well with their relative expression levels at four stages, suggesting the involvement of epigenetics in transcriptional regulation. A striking finding is that seed germination-specific genes start to show open chromatin (H3K4me3) during late seed maturation although their transcripts do not accumulate, which is further supported by RNA polymerase II binding. Together, our results provide the first evidence that seed germination genes can be primed for transcription (open chromatin and RNA polymerase II binding) during seed maturation, highlighting that the transition from seed maturation to seed germination starts at late seed maturation stages at both the genetic and epigenetic levels.
2011-05-10 | GSE29134 | GEO
Project description:Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we measured gene expression levels of Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using. We mapped the eQTL of the gene expression and the result displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
2020-06-24 | E-MTAB-9080 | biostudies-arrayexpress
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition. Transcriptome, chromatin accessibility, H3.3 and H2A.Z enrichment, and DNA methylation were examined in Col or h3.3ko mutant
2022-12-01 | GSE209642 | GEO
Project description:Regulation of seed germination by dormancy relies on a complex network of transcriptional and post‐transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High‐throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway‐based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non‐dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination.
2019-05-21 | MTBLS662 | MetaboLights