Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1033393 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26559008_1.fastq.gz | Fastqsanger.gz | |||
| SRR26559008_2.fastq.gz | Fastqsanger.gz | |||
| SRR26559009_1.fastq.gz | Fastqsanger.gz | |||
| SRR26559009_2.fastq.gz | Fastqsanger.gz | |||
| SRR26559010_1.fastq.gz | Fastqsanger.gz |
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Project description:Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil. However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. Here we aim at understand the genotypic differences in two rice cultivars with contrasting phenotypes under Fe toxicity.
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Project description:One of the serious constraints to realize high level of rice crop productivity in agriculture has been due to Soil Water Stress (SWS) situation that growing plants often face. In order to increase or maintain the crop productivity in SWS situation, our initial aim is to understand the drought response mechanism in different genotypes of rice. For thorough analysis of SWS situation in rice we have taken here two wild genotypes of rice namely Oryza nivara, Oryza rufipogon and three Oryza sativa indica cultivars namely Nagina-22, IR20 and Vandana, where IR20 is known to be susceptible and Vandana is known to be tolerant under SWS condition [GSE49364 and the current study]. Global analysis of transcript profiling under SWS condition reveal the actual picture of genes responsive to stress situation in different genetic background of rice. Furthermore it would help us in the selection of most desirable resource for crop breeding without compromising the yield of crop. We used the 44k rice Oligoarray from Agilent technologies to study the expression profiles from five rice genotypes during vegetative (Veg) and grain-filling (GF) stages under varying water conditions, viz. Before Stress (BS), After Stress (AS) and After Recovery (AR).
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Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants.
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Project description:We used RNA-Seq to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 concentration and by the transcription regulator CIA5(CCM1). Both CO2 concentration and CIA5 are known to play roles in induction of an essential CO2-concentrating mechanism (CCM), but the degree of interaction and the extent of global regulation beyond the CCM were not previously understood. We compared the transcriptome of a wild type strain vs. a cia5 strain under 3 CO2 supply conditions: high CO2 (H-CO2; 5%); low CO2 (L-CO2; 0.03 to 0.05%); and very-low CO2 (VL-CO2; <0.02%). Our goals were to: 1) reveal candidate genes that, through changes in their expression, distinguish multiple acclimation states induced by H-CO2, L-CO2, and VL-CO2; 2) reveal genes regulated directly or indirectly by CIA5; and 3) reveal genes responding to the interaction between CIA5 and changes in CO2 concentration. Our results revealed a small group of genes as encoding putative Ci transporters based on their expression patterns. The results also showed a massive and much broader impact on global gene regulation by CIA5/CCM1, which directly or indirectly affected 15% of the Chlamydomonas genome. The transcriptomes under L-CO2 and VL-CO2 conditions were not significantly different, suggesting that these two acclimation states must be controlled by mechanisms operating beyond transcript abundance.
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