Systemic suppression of the rice shoot metabolism upon root rot nematode infection
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ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE57707 | GEO | 2015/05/18
SECONDARY ACCESSION(S): PRJNA247782
REPOSITORIES: GEO
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Project description:Rice (Oryza sativa L.) is one of the most important staple foods in the world, feeding more than 50% of the human population. One of its most damaging pathogens, with major impact on rice yield, is the migratory root rot nematode Hirschmanniella oryzae. In comparison with the existing knowledge on the infection process of dicots by sedentary nematodes, far less is known about the interaction between monocot plants and nematodes or plant interactions with migratory nematode species. Therefore, to gain deeper insight into the systemic transcriptional changes in rice after migratory root rot nematode infection we have performed mRNA-Seq on the shoots of root rot nematode infected rice plants. The observations were independently validated using qRT-PCR and biochemical analyses. This research reveals significant modifications in the metabolism of the plant, with a general suppression of chlorophyll biosynthesis, and primary metabolic processes involved in plant growth . Differential expression analysis between controls rice shoots and shoots from root rot nematode (H. oryzae) infected rice at two time points.
2015-05-18 | E-GEOD-57707 | biostudies-arrayexpress
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.
2013-01-10 | GSE35843 | GEO
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: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
2013-08-07 | E-GEOD-43577 | biostudies-arrayexpress
Project description:There is mounting evidence for the role of epigenetic processes in the regulation of plant responses to a wide range of external stimuli. Despite their importance, the significance of epigenetic processes in plant-pathogen interactions remain poorly understood. So far, the role of histone modifications has not been investigated at genome wide level in plant-nematode interactions, although their expression levels are altered in nematode-induced galls. In this study, we first applied chemical inhibitors of histone modifying enzymes on rice plants. Despite theirdistinct effects on histone modifications, application of different concentrations of Niconinamide, sulfamethazine and fumaric acid lead to reduced susceptibility to nematode infection. Similarly, two overexpression lines of histone lysine methyltransferases and one histone deacetylase were analyzed in an infection assay with nematodes, showing contrasting results in susceptibility. These data indicate that histone modifications can affect plant defence against nematodes in rice. To further investigate their effect, the genome-wide level of three histone marks namely H3K9ac, H3K9me2 and H3K27me3 was studied by chromatin-immunoprecipitation (ChIP)-sequencing on nematode-induced galls in comparison with control root tips.
2021-02-17 | GSE145501 | GEO
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.
2013-08-07 | GSE43577 | GEO
Project description:Magnaporthe oryzae (rice blast) and the root-knot nematode Meloidogyne graminicola are causing two of the most important pathogenic diseases jeopardizing rice production. Here, we show that root-knot nematode infestation on rice roots leads to important above-ground changes in plant immunity gene expression, which is correlated with significantly enhanced susceptibility to blast disease.
2018-11-02 | GSE89449 | GEO
Project description:Background: Epigenetic processes play an important role in the plant response to adverse environmental conditions. A role for DNA hypomethylation has recently been suggested in the pathogenic interaction between bacteria and plants, yet it remains unclear whether this phenomenon reflects a conserved and general plant immunity response. We therefore investigated the role of DNA methylation in the plant defence against damaging parasitic nematodes. Methods and results: Treatment of roots of rice (monocot plant) and tomato (dicot plant) by a nematode-associated molecular pattern (NAMP) from different parasitic nematodes revealed global DNA hypomethylation using ELISA based quantification, suggesting conservation among plants. Focusing on root-knot induced gall tissue in rice, the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon 5-Azacitidine treatment. Whole genome bisulfite sequencing revealed that hypomethylation was massively present in the CHH context, while absent for CpG or CHG nucleotide contexts. CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point, but rather showed a delayed effect on transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway (RdDM) and DDM1, which are known to be steering DNA methylation in CHH context. Conclusions: We demonstrated that DNA hypomethylation confers enhanced defence in rice towards root-parasitic nematodes and is likely to be part of the basal NAMP-triggered immunity response in plants.
2020-07-07 | GSE130064 | GEO
Project description:During a compatible interaction, root-knot nematodes (Meloidogyne spp.) induce the redifferentiation of root cells into multinucleate nematode feeding cells giant cells. These hypertrophied cells result from repeated nuclear divisions without cytokinesis, are metabolically active and present features typical of transfer cells. Hyperplasia of the surrounding cells leads to formation of the typical root gall. We investigate here the plant response to root-knot nematodes.
2005-01-11 | E-MEXP-233 | 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
2011-09-24 | E-GEOD-21772 | biostudies-arrayexpress