Ontology highlight
ABSTRACT:
PROVIDER: PRJNA576043 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10239313_1.fastq.gz | Fastqsanger.gz | |||
| SRR10239313_2.fastq.gz | Fastqsanger.gz | |||
| SRR10239314_1.fastq.gz | Fastqsanger.gz | |||
| SRR10239314_2.fastq.gz | Fastqsanger.gz | |||
| SRR10239315_1.fastq.gz | Fastqsanger.gz |
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Project description:A biological phenomenon in which hybrids exhibit superior phenotypes from its parental inbred lines known as heterosis, has been widely exploited in plant breeding and extensively used in crop improvement. Hybrid rice has immense potential to increase yield over other rice varieties and hence is crucial in meeting increasing demand of rice globally. Moreover, the molecular basis of heterosis is still not fully understood and hence it becomes imperative to unravel its genetic and molecular basis. In this context, RNA sequencing technology (RNA-Seq) was employed to sequence transcriptomes of two rice hybrids, Ajay and Rajalaxmi, their parental lines, CRMS31A (sterile line, based on WA-CMS) and CRMS32A (sterile line based on Kalinga-CMS) respectively along with the common restorer line of both hybrids, IR-42266-29-3R at two critical rice developmental stages viz., panicle initiation (PI) and grain filling (GF). Identification of differentially expressed genes (DEGs) at PI and GF stages will further pave the way for understanding heterosis. In addition, such kind of study would help in better understanding of heterosis mechanism and genes up-regulated and down-regulated during the critical stages of rice development for higher yield.
2015-08-02 | E-MTAB-4291 | biostudies-arrayexpress
Project description:Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types at three different developmental stages, we obtained a much more comprehensive view of genes that related to rice heterosis and analyzed the potential effects of gene-expression difference on the heterosis of rice.These heterotic expression genes among different genotypes provided new avenues for exploring the molecular mechanisms underlying heterosis, including variable gene expression patterns. Keywords: Heterosis study by SAGE
2007-06-08 | GSE8048 | GEO
Project description:Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types at three different developmental stages, we obtained a much more comprehensive view of genes that related to rice heterosis and analyzed the potential effects of gene-expression difference on the heterosis of rice.These heterotic expression genes among different genotypes provided new avenues for exploring the molecular mechanisms underlying heterosis, including variable gene expression patterns. Keywords: Heterosis study by SAGE We constructed nine SAGE libraries parallelly, including root at the first tillering stage, leaf at the milky stage of rice grain maturation, and panicle at the pollen-maturing stage of hybrid rice (LYP9) and its paternal lines (9311, PA64s).
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Project description:Heterosis and polyploidy are two important aspects of plant evolution. To examine these issues, we conducted a global gene expression study of a maize ploidy series as well as a set of tetraploid inbred and hybrid lines. This gene expression analysis complements an earlier phenotypic study of these same materials. We find that ploidy change affects a large fraction of the genome, albeit at low levels; gene expression changes rarely exceed 2-fold and are typically not statistically significant. The most common gene expression profile we detected is greater than linear increase from monoploid to diploid, and reductions from diploid to triploid and from triploid to tetraploid, a trend that mirrors plant stature. When examining heterosis in tetraploid maize lines, we found a large fraction of the genome impacted but the majority of changes were not statistically significant at 2-fold or less. Non-additive expression was common in the hybrids, and the extent of non-additivity increased both in number and magnitude from duplex to quadruplex hybrids. Overall, we find that gene expression trends mirror observations from the phenotypic studies; however, obvious mechanistic connections remain unknown. We examined gene expression in a ploidy series (1n to 4n) of the maize line B73 and in a variety of hybrid tetraploid lines using a complex loop design. Pooled RNA samples from 10 plants were used (2 independent RNA isolations/sample), and all comparisons were made using replicate dye swaps (16 slide sets/comparison). For the ploidy analysis, all expression changes were computed relative to the diploid as well as between 2n + 3n and 3n + 4n. For the expression analysis of hybrids, hybrid expression levels were compared to the parental expression levels as well as to mid-parent levels.
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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.
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Project description:Heterosis and polyploidy are two important aspects of plant evolution. To examine these issues, we conducted a global gene expression study of a maize ploidy series as well as a set of tetraploid inbred and hybrid lines. This gene expression analysis complements an earlier phenotypic study of these same materials. We find that ploidy change affects a large fraction of the genome, albeit at low levels; gene expression changes rarely exceed 2-fold and are typically not statistically significant. The most common gene expression profile we detected is greater than linear increase from monoploid to diploid, and reductions from diploid to triploid and from triploid to tetraploid, a trend that mirrors plant stature. When examining heterosis in tetraploid maize lines, we found a large fraction of the genome impacted but the majority of changes were not statistically significant at 2-fold or less. Non-additive expression was common in the hybrids, and the extent of non-additivity increased both in number and magnitude from duplex to quadruplex hybrids. Overall, we find that gene expression trends mirror observations from the phenotypic studies; however, obvious mechanistic connections remain unknown.
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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.
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