Oryza sativa Japonica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA186751 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR650322_1.fastq.gz | Fastqsanger.gz | |||
| SRR650322_2.fastq.gz | Fastqsanger.gz | |||
| SRR650323_1.fastq.gz | Fastqsanger.gz | |||
| SRR650323_2.fastq.gz | Fastqsanger.gz | |||
| SRR650324_1.fastq.gz | Fastqsanger.gz |
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2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
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 6 arrays - rice
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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:affy_meloidogyne_rice - affy_meloidogyne_rice - Plant-parasitic nematodes cause profound economic losses to global agriculture with the obligate sedentary endoparasitic varieties; amongst them the cyst and Root Knot Nematode (RKN) species are the most damaging. Meloidogyne graminicola is a RKN mainly found in the monocotyledous plants. In the compatible interaction with Oryza sativa, M. graminicola induces the characteristic formation of hook-like galls resulting from the redifferentiation of root cells into multinucleate giant cells. In order to understand the global transcriptome changes occurring during infection, several recent microarray studies on root knots have demonstrated complex changes in host plant gene expression in response to infection. However, to our knowledge, all these transcriptome studies were performed on dicotyledous plants. A histological study enabled us to observe hyperplasia and hypertrophy of the surrounding cells leading to the formation of hook-like galls. We also investigated the plant response to M. graminicola by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at an early stage (2dpi) and a latter stage (4dpi) 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 5 days before being inoculated with a 100 J2-stage juveniles M. graminicola. 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 2 and 4 dai and each of them contained galls from 70 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,time course 9 arrays - rice
2011-09-24 | E-GEOD-21919 | biostudies-arrayexpress
Project description:affy_meloidogyne_rice - affy_meloidogyne_rice - Plant-parasitic nematodes cause profound economic losses to global agriculture with the obligate sedentary endoparasitic varieties; amongst them the cyst and Root Knot Nematode (RKN) species are the most damaging. Meloidogyne graminicola is a RKN mainly found in the monocotyledous plants. In the compatible interaction with Oryza sativa, M. graminicola induces the characteristic formation of hook-like galls resulting from the redifferentiation of root cells into multinucleate giant cells. In order to understand the global transcriptome changes occurring during infection, several recent microarray studies on root knots have demonstrated complex changes in host plant gene expression in response to infection. However, to our knowledge, all these transcriptome studies were performed on dicotyledous plants. A histological study enabled us to observe hyperplasia and hypertrophy of the surrounding cells leading to the formation of hook-like galls. We also investigated the plant response to M. graminicola by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at an early stage (2dpi) and a latter stage (4dpi) 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 5 days before being inoculated with a 100 J2-stage juveniles M. graminicola. 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 2 and 4 dai and each of them contained galls from 70 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,time course
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Project description:In this study a comparison was made between the local transcriptional changes at two time points upon root knot (Meloidogyne graminicola) and migratory nematode (Hirschmanniella oryzae) infection in rice. Using mRNA-Seq we have characterized specific and general responses of the root challenged with these endoparastic root nematodes with very different modes of action. Root knot nematodes induce major developmental reprogramming of the root tip, where they force the cortical cells to form multinucleate giant cells, resulting in gall-development. Our results show that root knot nematodes force the plant to produce and transfer nutrients, like sugars and amino acids, to this tissue. Migratory nematodes, on the other hand, induce the expression of proteins involved in plant death and oxidative stress, and obstruct the normal metabolic activity of the root. While migratory nematode infection also causes upregulation of biotic stress-related genes early in the infection, the root knot nematodes seem to actively suppress the local defence of the plant root. This is exemplified by a downregulation of genes involved in the salicylic acid and ethylene pathways. Interestingly, hormone pathways usually involved in plant development, were strongly induced (auxin and gibberellin) or repressed (cytokinin) in the galls. In addition, thousands of novel transcriptionally active regions as well as highly expressed nematode transcripts were detected in the infected root tissues. These results uncover previously unrecognized nematode-specific expression profiles and provide an interesting starting point to study the physiological function of many yet unannotated transcripts potentially targeted by these nematodes. 2 or 3 biological replicates of nematode infected roots and root tips and their respective controls were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)
2013-01-10 | E-GEOD-35843 | biostudies-arrayexpress
Project description:Below ground attack by root knot nematode Meloidogyne graminicola predisposes rice to blast disease
| PRJNA352238 | ENA
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. Control condition experiment, root or shoot of WT vs. MIT knockdown plant. Two replicates each comparison, including a dye swap.
2011-04-07 | E-GEOD-28428 | biostudies-arrayexpress