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Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome Analysis of Wounding-Induced Root to Shoot Communication in Arabidopsis thaliana.

ABSTRACT: Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS). Two-condition experiment, shoots of root-wounded seedlings vs. shoots of control seedlings. Biological replicates: 2 control replicates, 2 treated replicates. Technical replicate: Dyeswap

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Takumi Nishiuchi

PROVIDER: E-GEOD-26374 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression analysis of wounding-induced root-to-shoot communication in Arabidopsis thaliana.

Hasegawa Satoko S Sogabe Yusuke Y Asano Tomoya T Nakagawa Tomoyuki T Nakamura Haruna H Kodama Hiroaki H Ohta Hiroyuki H Yamaguchi Kazuo K Mueller Martin J MJ Nishiuchi Takumi T

Plant, cell & environment 20110315 5

Root-to-shoot communication plays an important role in the adaptation to environmental stress. In this study, we established a model system for root-to-shoot signalling to observe global gene expression in Arabidopsis thaliana. The roots of Arabidopsis seedlings were wounded and the expression in the shoots of 68 and 5 genes was up-regulated threefold at 30 min and 6 h post-injury, respectively. These genes were designated early and late Root-to-Shoot responsive (RtS) genes, respectively. Many o ...[more]

PMID: 21241326

Similar Datasets

Transcriptome Analysis of Wounding-Induced Root to Shoot Communication in Arabidopsis thaliana.

Project description:Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS).

2010-12-31 | GSE26374 | GEO

Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and a microarray

Project description:Aerenchyma is a specialized tissue consisting of longitudinal gas spaces, which enables internal movement of gases (e.g., O2, CO2, ethylene and methane), in plant roots, petioles and stems. Especially, internal transport of oxygen via aerenchyma from shoots to roots is very important for adaptation or survival of plants under waterlogged condition. To identify aerenchyma formation-associated genes expressed in maize root, we used LM combined with a microarray for monitoring genes expressed in root cortical cells under three conditions: under aerobic condition and under waterlogged condition with and without pretreatment with 1-MCP, an inhibitor of ethylene perception. For the waterlogging treatments, the primary root (but not the shoots) was waterlogged. Two and half day-old-seedlings were pre-treated with an inhibitor of ethylene perception 1-methylcyclopropene (1-MCP; 1 ppm) for 12 hours before the waterlogging treatment. Three-day-old seedlings were growing under aerated condition at the same time with other treatments as a control. Total RNA was extracted from root cortex cells from the segment of the primary root, 0.5 cm long: from 1.5 to 2 cm from the junction shoot-root derived from 3-days-old maize seedlings, and subjected to 44k oligo-DNA microarray (1. Aerated vs Hypoxia, 2. Hypoxia+MCP vs Hypoxia) with 3 biological replicates and color swaps.

2010-07-31 | E-GEOD-22943 | biostudies-arrayexpress

Redox regulation of auxin and strigolactone signaling in the control of Arabidopsis thaliana root growth

Project description:Reduced glutathione (GSH) is required for cell cycle initiation and auxin-regulated root meristem development. Transcriptome profiling of the roots and shoots of the root meristemless 1 (rml1) mutant, which has about 3% of the wild type GSH, revealed a divergent auxin and strigolactone response linked to the arrest of the cell cycle. Plants of the rml1 mutant and Columbia-0 ecotype were harvested and separated into roots and shoots, then RNA extraction and Affymetrix Agronomics Tiling Array were performed.

2013-01-10 | E-GEOD-36893 | biostudies-arrayexpress

Insights into Transcriptional Regulatory Pathways on Systemic Communication under Flooding in Arabidopsis

Project description:We analyzed global transcriptional changes in both shoots and roots of root-flooded Arabidopsis seedlings by microarrays. We also interpreted the significance of the systemic communication between roots and shoots by functional classification of affected genes. We performed genetic analysis with an ethylene signaling mutant, ein2-5, to correlate systemic flooding responses with ethylene signaling. We identified a class of genes that were up- or downregulated in shoots, but not affected in roots, under hypoxic conditions. A comprehensive managing program of carbohydrate metabolism was observed, providing an example of how systemic communications might facilitate the survival of plants under flooding. A proportion of long-distance hypoxic regulation was altered in ein2-5. Time course experiments (0.5, 1, 3, 6, and 12h for Columbia; 0.5, 3, and 6h for ein2-5). Tissues from root-flooded seedlings vs. Tissues from un-flooded seedlings. Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array. 2 of 4 replicates are dye-swapped.

2011-10-20 | E-GEOD-28885 | biostudies-arrayexpress

RNA-Seq and BS-Seq of Sorghum bicolor tissues

Project description:This study utilized next generation sequencing technology (RNA-Seq and BS-Seq) to examine the transcriptome and methylome of various tissues within sorghum plants with the ultimate goal of improving the Sorghum bicolor annotation We examined the mRNA of various Sorghum bicolor (BTx623) tissues (flowers, vegitative and floral meristems, embryos, roots and shoots) and bisulfite treated DNA from two root samples

2014-08-29 | E-GEOD-50464 | biostudies-arrayexpress

Transcriptomic study of the impact of iron toxicity on rice plant

Project description:transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv M-bM-^@M-^XI Kong PaoM-bM-^@M-^Y ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm). Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and 3 weeks in hydroponic culture. Comparison between control and iron stressed plants were done at the shoot and the root levels. The assays were replicated twice on two independent plant cultures. 8 samples, Two-condition experiment, control (0 ppm ferrous iron) vs. iron treated (125 ppm ferrous iron). Biological replicates: 2 replicates for comparison shoot 3 days of stress, root 3 days of stress, shoot 3 weeks of stress and root 3 weeks of stress.

2012-05-14 | E-GEOD-36299 | biostudies-arrayexpress

Determination of genes expressed in response to drought in root and shoot of Leucaena leucocephala

Project description:Leucaena leucocephala seedlings were treated with PEG6000 and the shoot and root tissues were collected after 48 hours following the treatment. The gene expressions were compared between treated and untreated in root and shoot separately. The differentially expressed genes may be related to drought resistance. RNA from shoot and root from treated and untreated L. leucocephala seedlings were extracted. Two biological replicates were made for each sample (each replicate represents about 10 individual seedlings).

2016-01-13 | E-GEOD-76810 | biostudies-arrayexpress

Expression data from Arabidopsis thaliana root and piriformaspora indica during log and short term interaction

Project description:Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant per-formance, growth and resistance/tolerance against abiotic and biotic stress. We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the gene expression pattern indicates a shift from defense to mutualistic interaction. We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the downregulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance. Twelve day-old (48 h cold treatment and 10 days of illumination) Arabidopsis seedlings of equal sizes were selected for co-cultivation experiments. They were transferred to PNM plates with a nylone membrane on the top (Johnson et al. 2011) and exposed to a fungal plug 5 mm in diameter or a KM plug of the same size without fungal hyphae (control). The plugs were placed 3 cm away from the closest root part . The light intensity (80 Â± 5 Î¼mol m-2 sec-1) was checked every third day to ensure that both P. indica- and mock-treated seedlings receive equal amounts of light.

2016-05-30 | E-GEOD-58771 | biostudies-arrayexpress

Systemic suppression of the rice shoot metabolism upon root rot nematode infection

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

Impact of rhamnolipids (RLs), natural defense elicitors, on shoot and root proteomes of Brassica napus by a Tandem Mass tags (TMTs) labeling approach

Project description:The rapeseed crop (Brassica napus) is valued mainly for animal feed, food oil and biofuel production. This plant is particularly susceptible to many pathogens like parasitic plants, fungi or animals attacking aerial or root parts. Conventional plant protection products, used intensively in agriculture, have a negative impact on the environment (air and water quality, biodiversity, etc.) as well as on human health. There is therefore a growing demand for the development of new, more planet-friendly alternative protection methods such as biocontrol compounds. Natural rhamnolipids (RLs) can be used as elicitors of plant defense mechanisms. Indeed, these glycolipids, from bacteria secretome, are biodegradable, non-toxic and they are known for their stimulating and protective effects, in particular on rapeseed against filamentous fungi. Characterizing the organ responsiveness to defense stimulating compounds like RLs is missing. This analysis is crucial in the frame of optimizing the effectiveness of RLs against various diseases. A TMT labeling of the proteins extracted from the shoots and roots of B. napus has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several protein families possibly involved in the differential responses observed in shoots and roots of rapeseed upon RLs treatment. In particular, quantitative proteomic analysis highlighted differential accumulation of parietal and cytoplasmic defense or stress proteins in response to treatments with RLs with a clear effect of the type of application (foliar spraying or root absorption). These results must be considered for further use of RLs to fight specific rapeseed pathogens.

2023-01-24 | PXD038531 | Pride

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