Oryza sativa Indica Group
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR209027_1.fastq.gz | Fastqsanger.gz | |||
| DRR209027_2.fastq.gz | Fastqsanger.gz | |||
| DRR209028_1.fastq.gz | Fastqsanger.gz | |||
| DRR209028_2.fastq.gz | Fastqsanger.gz |
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Project description:Identification of the mutation associated with reduced seed shattering in a high-yielding indica rice cultivar 'Oonari'
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Project description:Domestication of indica rice has facilitated better harvest and yield, however the molecular mechanisms that drove multitude of phenotypes is not fully understood. A few genetic mechanisms such as sequence variations as well as small (s)RNAs and epigenetics have been attributed to indica rice domestication, but upstream regulators of these variations are unknown. Here we identified a copper (Cu) dependent regulatory module involved in the regulation of a SPL family transcription factor (TF) as well as two classes of RNAs under its direct control. Differential accumulation of Cu-associated micro (mi)RNAs and Cu-associated protein-coding RNAs were a major portion of the differences between wild relative of indica rice (Oryza nivara) and cultivated rice lines. We identified OsSPL9 as an upstream regulator of these changes through genetic and molecular analysis as well as by using Cu limited and excess conditions. OsSPL9 bound to the promoters of these genes through a conserved GTAC enriched motif. OsSPL9, Cu-associated miRNAs and their targets were in a regulatory loop, since mis-expression of SPL9 alone, or any individual Cu-associated miRNA also altered levels of other Cu-associated miRNAs and their cognate targets. OsSPL9 mediated regulation was closely linked to Cu accumulation and metabolism, indicating previously unappreciated roles of metal ions in mediating domestication-associated phenotypes. Our study has the potential to facilitate a better understanding of the crosstalk between genetic and epigenetic regulation that contributed to rice domestication connected to altered environment and growth conditions.
2026-04-27 | GSE292471 | GEO
Project description:Domestication of indica rice has facilitated better harvest and yield, however the molecular mechanisms that drove multitude of phenotypes is not fully understood. A few genetic mechanisms such as sequence variations as well as small (s)RNAs and epigenetics have been attributed to indica rice domestication, but upstream regulators of these variations are unknown. Here we identified a copper (Cu) dependent regulatory module involved in the regulation of a SPL family transcription factor (TF) as well as two classes of RNAs under its direct control. Differential accumulation of Cu-associated micro (mi)RNAs and Cu-associated protein-coding RNAs were a major portion of the differences between wild relative of indica rice (Oryza nivara) and cultivated rice lines. We identified OsSPL9 as an upstream regulator of these changes through genetic and molecular analysis as well as by using Cu limited and excess conditions. OsSPL9 bound to the promoters of these genes through a conserved GTAC enriched motif. OsSPL9, Cu-associated miRNAs and their targets were in a regulatory loop, since mis-expression of SPL9 alone, or any individual Cu-associated miRNA also altered levels of other Cu-associated miRNAs and their cognate targets. OsSPL9 mediated regulation was closely linked to Cu accumulation and metabolism, indicating previously unappreciated roles of metal ions in mediating domestication-associated phenotypes. Our study has the potential to facilitate a better understanding of the crosstalk between genetic and epigenetic regulation that contributed to rice domestication connected to altered environment and growth conditions.
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Project description:Rice genome resequecing to identify responsible loci (mutation) detection for BRITTLE CULM mutants
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Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.
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Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication. Non-coding small RNA were generated from three different tissues of O.rufipogon by sequecing using Illumina GAII
2012-08-10 | E-GEOD-39308 | biostudies-arrayexpress
Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.
2012-08-10 | GSE39307 | GEO
Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication. The 5' end of the 3' degraded mRNAs with polyA tails were collected and generated from seedlings at four-leaves stage of O.rufipogon by degradome highthoughput sequecing using Illumina GAII
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