E-GEOD-43727
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-43727 | ExpressionAtlas | 2020-04-01
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-43727-analysis-methods.tsv | Tabular | |||
| E-GEOD-43727-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-43727-coexpressions.tsv.gz | Tabular | |||
| E-GEOD-43727-configuration.xml | Xml | |||
| E-GEOD-43727-factors.xml | Xml |
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Project description:Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis. We constructed six sRNA sequencing libraries and six mRNA sequencing libraries of flag leaves and panicles of the super-hybrid rice Liangyou-pei9 (LYP9) combination at the grain-filling stage. The above hybrid rice combination includes F1 hybrid LYP9 and its parental lines including the male-sterile line Peiai64s (PA64s) and the restorer line 93-11.
2014-08-17 | E-GEOD-51468 | biostudies-arrayexpress
Project description:To study the function of chromatin regulators in hybrid gene expression, the histone deacetylase gene OsHDT1 was over-expressed or inactivated by RNAi in an elite rice parent. Digital analysis of gene expression using high throughput sequencing technology revealed several differential gene expression patterns in the hybrid, including additivity, nonadditivity and overdominance, etc. Alteration of OsHDT1 levels affected many genes specifically in the hybrid. In addition, we show that increased OsHDT1 could suppress overdominance gene expression, providing evidence of overdominance gene action in heterosis. These results not only support the overdominance hypothesis to explain heterosis, but also provide evidence that variation in the levels of single trans-acting regulatory proteins such as chromatin factors is important to establish differential gene expression pattern in the hybrid. High throughput sequencing technology was used to analyse gene differencial expression of 15 days old rice seedling of 5 samples, MH63(MH), ZS97(ZS), SY63(SY,hybrids of MH and ZS), overexpression of OsHDT1 in SY(FU), RNAi of OsHDT1 in SY(FR).
2012-01-01 | E-GEOD-27240 | biostudies-arrayexpress
Project description:Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis.
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Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone H3 trimethylation in rice endosperm. By obtaining about four hundred million bases of sequence from rice chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of rice endosperm. We find that the presence of H3K27me3 in either upstream or downstream of a gene is predominately associated with repression of the gene, while its absence is mainly associated with high gene expression. Examination of Histone H3 lysine 27 trimethylation in rice endosperm.
2011-12-06 | E-GEOD-27048 | biostudies-arrayexpress
Project description:Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations Keywords: Expression profiling by high throughput sequencing
2010-03-01 | GSE16631 | GEO
Project description:Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations Keywords: Expression profiling by high throughput sequencing mRNA expression of 8 independent rice tissues was determined by method of RNA-Seq using short reads from high throughput sequencing technology. Meanwhile small RNA populations from mixture solution pooled from total RNA of each 8 tissues were also sequenced.
2010-03-01 | E-GEOD-16631 | biostudies-arrayexpress
Project description:Heterosis is a phenomenon that hybrids exhibit superior performance relative to the parental phenotypes. However, most studies focused on aboveground agronomic traits. Thus, systematic investigation on root heterosis, particularly at reproductive stage in rice is needed to be carried out. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis study.Using the Illumina HiSeq 2000 platform, the root transcriptome of a super-hybrid rice Xieyou9308 and its parents were analyzed at tillering and heading stages. Totally, 829 and 4186 differentially expressed genes between the hybrid and its parents (DGHP) were detected at tillering stage and heading stage, respectively. In this study, the DGHP were significantly enriched in pathways such as carbohydrate metabolism and plant hormones signal transduction at heading stage, and most of the key genes involved in the two pathways were up-regulated in the hybrid. Several significant DGHP that could be mapped to QTLs for yield and root traits were also involved in carbohydrate metabolism and plant hormones signal transduction pathways. The candidate transcripts may underlie the heterosis and significantly contribute to root development and yield production. Root mRNA profiles of a super-hybrid rice Xieyou 9308 and its parents at tillering and heading stages were generated by deep sequencing, in duplicate, on Illumina Hiseq 2000 platform.
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Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone H3 trimethylation in rice endosperm. By obtaining about four hundred million bases of sequence from rice chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of rice endosperm. We find that the presence of H3K27me3 in either upstream or downstream of a gene is predominately associated with repression of the gene, while its absence is mainly associated with high gene expression.
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