Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA181348 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR618545.fastq.gz | Fastqsanger.gz | |||
| SRR618546.fastq.gz | Fastqsanger.gz | |||
| SRR618547.fastq.gz | Fastqsanger.gz | |||
| SRR618548.fastq.gz | Fastqsanger.gz | |||
| SRR618549.fastq.gz | Fastqsanger.gz |
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Project description:Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability. Whole genome methylation maps of rice were generated using BS-seq (Hume Stroud, Suhua Feng, Steve Jacobsen at UCLA). Whole genome expression maps of rice were generated using mRNA-seq and smRNA (Stacey Simon, Blake Meyers at Univ of Delaware).
2013-03-26 | E-GEOD-42410 | biostudies-arrayexpress
Project description:Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability.
2013-03-26 | GSE42410 | GEO
Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164584 | GEO
Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164583 | GEO
Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.
2021-08-27 | GSE164582 | GEO
Project description:Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.
2023-01-06 | GSE196869 | GEO
Project description:Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.
2023-01-06 | GSE196868 | GEO
Project description:affy_meloidogyne_rice2 - affy_meloidogyne_rice2 - Plant-parasitic nematodes cause heavy economic losses to global agriculture. The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. M. incognita infection to dicotyledous plants is extensively studied but it is also important to study their interaction with monocotyledous plants, in particular with cereals. In our growing conditions, as of day 6, histological studies revealed a profound rice tissue reorganisation around nematodes, notably characterized by the plant feeding site formation. We are investigating the molecular plant response to M. incognita by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at this early stage (6dpi) of gall development-Oryza sativa (var. Nipponbare) seedlings were grown on 6 cm3 SAP substrate completed with diluted Hoaglands solution (Reversat et al., 1999). Culture units were placed in a growth chamber illuminated with fluorescent tubes 9/24 h and maintained at 23°C for 6 days before being inoculated with a 300 J2-stage juveniles M. incognita. One day after inoculation (dai), the rice seedlings were immersed in de-ionised water to remove all J2s that had not penetrated the roots and allowing synchronization of the infection. Each seedling was transferred to a hydroponic mini chamber (Reversat et al., 2004). Sampling was performed at 6 dai and each of them contained galls from 45 infected plants, they were then hand-dissected, frozen in liquid-nitrogen and stored at -80°C. As reference samples, uninfected meristematic root fragments were dissected from seedlings grown under the same conditions. Each sample was replicated 3 times. Keywords: normal vs disease comparison
2011-09-25 | GSE21772 | GEO
Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.
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Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.
2011-04-07 | GSE28428 | GEO