Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1133942 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30004316_1.fastq.gz | Fastqsanger.gz | |||
| SRR30004316_2.fastq.gz | Fastqsanger.gz | |||
| SRR30004317_1.fastq.gz | Fastqsanger.gz | |||
| SRR30004317_2.fastq.gz | Fastqsanger.gz | |||
| SRR30004318_1.fastq.gz | Fastqsanger.gz |
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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: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: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.
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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. Illumina sequencing of transcripts from cotyledons of mid-maturation (B1 stage) and late maturation (AA1 stage) seeds, whole dry seeds, and cotyledons of seedlings six days after imbibition.
2011-05-10 | E-GEOD-29134 | biostudies-arrayexpress
Project description:Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize
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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:Seed germination represents a critical developmental transition in spermatophytes. Gibberellins (GAs) are essential phytohormones regulating seed germination. GA2-oxidases (GA2ox) play a key role in modulating GA levels by converting active GAs to inactive forms, critically influencing seed development and germination. How seed germination is epigenetically regulated by DNA methylation is poorly understood. Here, we identified the tomato methyl-CpG-binding domain (MBD) protein SlMBD5 as a regulator of seed germination. The slmbd5 mutant exhibits delayed germination and reduced GA4/GA7 levels, which can be rescued by exogenous GA4+7 application. Transcriptomic and biochemical analyses revealed that SlMBD5 represses the GA catabolism gene SlGA2ox4 by directly binding to its hypermethylated promoter. Furthermore, we show that SlMBD5 interacts with the histone methylation reader SlEBS, forming a functional complex that promotes the transcriptional repression of SlGA2ox4. Consistent with the model that SIMBD5 promotes seed germination through its repression of SlGA2ox4, the slmbd5/slga2ox4 double mutant shows partially restored germination. This study thus reveals an SlMBD5-SlEBS module that epigenetically regulates GA homeostasis to modulate seed germination in tomato.
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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.
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