Unknown,Transcriptomics,Genomics,Proteomics

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Oryza sativa genes expressed in the early compatible interaction with root-knot nematode (affy_meloidogyne_rice)

ABSTRACT: 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

ORGANISM(S): Oryza sativa

SUBMITTER: sandrine balzergue

PROVIDER: E-GEOD-21919 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Biotrophic plant pathogens have evolved sophisticated strategies to manipulate their host. They derive all of their nutrients from living plant tissues, by making intimate contact with their host while avoiding a resistance response. Rice is one of the most important crop plants worldwide and an excellent model system for studying monocotyledonous plants. Estimates of annual yield losses due to plant-parasitic nematodes on this crop range from 10 to 25% worldwide. One of the agronomically most important nematodes attacking rice is the rice root knot nematode Meloidogyne graminicola. Attack of plant roots by sedentary plant parasitic nematodes, like the root knot nematodes (RKN; Meloidogyne spp.) involves the development of specialized feeding cells in the vascular tissue. The second stage juvenile of the RKN punctures selected vascular cells with its stylet, injects pharyngeal secretions, and this ultimately leads to the reorganisation of these cells into typical feeding structures called giant cells (GCs), from which the nematode feeds for the remainder of its sedentary life cycle (Gheysen & Mitchum, 2011). Morphological and physiological reprogramming of the initial feeding cell leads to nucleus enlargement, proliferation of mitochondria and plastids, metabolic activation, cell cycle alterations and cell wall changes (Gheysen and Mitchum, 2011). The hyperplasia and hypertrophy of the surrounding cells leads to the formation of a root gall, which is typically formed at the root tips in the case of the rice RKN M. graminicola. In comparison with other RKN, M. graminicola has a very fast life cycle, with swelling of the root tips observed as early as 1 day after infection (dai). At 3 dai, terminal hook-like galls are clearly visible (Bridge et al., 2005). After 3 moults the nematodes are mature, around 10 dai. The M. graminicola females lay their eggs inside the galls, while most other RKN deposit egg masses at the gall surface, and hatched juveniles can reinfect the same or adjacent roots. In well-drained soil at 22-29 degrees C the life cycle of M. graminicola is completed in 19 days. 2 biological replicates of nematode infected giant cells and control vascular cells were sampled at two time points: 7 and 14 dai

Project description:Biotrophic plant pathogens have evolved sophisticated strategies to manipulate their host. They derive all of their nutrients from living plant tissues, by making intimate contact with their host while avoiding a resistance response. Rice is one of the most important crop plants worldwide and an excellent model system for studying monocotyledonous plants. Estimates of annual yield losses due to plant-parasitic nematodes on this crop range from 10 to 25% worldwide. One of the agronomically most important nematodes attacking rice is the rice root knot nematode Meloidogyne graminicola. Attack of plant roots by sedentary plant parasitic nematodes, like the root knot nematodes (RKN; Meloidogyne spp.) involves the development of specialized feeding cells in the vascular tissue. The second stage juvenile of the RKN punctures selected vascular cells with its stylet, injects pharyngeal secretions, and this ultimately leads to the reorganisation of these cells into typical feeding structures called giant cells (GCs), from which the nematode feeds for the remainder of its sedentary life cycle (Gheysen & Mitchum, 2011). Morphological and physiological reprogramming of the initial feeding cell leads to nucleus enlargement, proliferation of mitochondria and plastids, metabolic activation, cell cycle alterations and cell wall changes (Gheysen and Mitchum, 2011). The hyperplasia and hypertrophy of the surrounding cells leads to the formation of a root gall, which is typically formed at the root tips in the case of the rice RKN M. graminicola. In comparison with other RKN, M. graminicola has a very fast life cycle, with swelling of the root tips observed as early as 1 day after infection (dai). At 3 dai, terminal hook-like galls are clearly visible (Bridge et al., 2005). After 3 moults the nematodes are mature, around 10 dai. The M. graminicola females lay their eggs inside the galls, while most other RKN deposit egg masses at the gall surface, and hatched juveniles can reinfect the same or adjacent roots. In well-drained soil at 22-29ºC the life cycle of M. graminicola is completed in 19 days.

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

Project description:Root-knot nematodes (RKN; Meloidogyne spp.) are sedentary parasites that affect a high variety of plants with a negative impact in the production of crops such as tomato. The infective RKN induces in the roots 4-7 highly specialized feeding cells (giant cells, GCs) developed into a hypertrophy cellular tissue or visible root swelling called M-bM-^@M-^\gallM-bM-^@M-^]. During GCs differentiation drastic alterations in genes expression occurs. However, information on genome-wide transcriptional profiles specifically in GCs is still lacking. With the aim to identify potential targets specifically regulated in GCs, we performed a temporal and spatial differential transcription profiling of tomato (Solanum lycopersicum), during the course of Meloidogyne javanica infection hybridizing TOM1 microarrays with hand-dissected galls at 1, 3, 7 and 14 days post-infection (dpi) and GCs exclusively isolated by LASER CAPTURE MICRODISSECTION (LCM) at 3 and 7 dpi. A GCs and galls comparison, at the same stage of development, reveals clear differences between their transcriptional patterns. For this purpose, a fast and efficient method to isolate LCM GCs from cryopreserved galls in the earliest differentiation state described to date: 48-72-hour post-infection (3 dpi), allowing good RNA preservation, was developed. In galls transcriptomic anaylsis, about 3000 galls and 4400 control uninfected root fragments were carefully hand-dissected at 1, 3, 7 and 14 dpi. Thus, more than 12 plates with 8 individual infected plants each, and 18 plates with the same number of plants as controls were used for only one independent experiment in each time point. Total RNA from two independent experiments was equimolarly pooled at each time of infection, in order to achieve a biological replicate for galls or control regardless. Therefore, a total of 6 independent experiments were performed to obtain 3 independent biological replicates for each infection point of galls and control analyzed. Following isolation, total RNA pooled from galls and control were subjected to a single round of linear amplification. In GCs transcriptomic analysis, independent biological replicates of aRNA from 300 GCs versus 600 control cells (CCs) from control root LCM at 3 and 7 dpi were obtained. Fifty GCs and 100 CCs were independently captured from sections onto separate CapSure HS LCM caps, and total RNA isolation was performed from each cap. RNA from six separate caps was pooled for a single biological replicate of GCs or CCs, respectively. In total, three independent biological replicates were processed. Thus, near to 7000 individual cells were harvested by LCM. The material was obtained from more that 18 independent infection experiments.

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Oryza sativa genes expressed in the early compatible interaction with root-knot nematode (affy_meloidogyne_rice)

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