Root hair-expressed genes in rice
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PROVIDER: PRJNA432070 | ENA |
REPOSITORIES: ENA
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Project description:root hair-expressed genes in rice
| PRJNA436704 | ENA
Project description:To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar
2018-03-03 | GSE111350 | GEO
Project description:To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar
2018-01-30 | GSE109811 | GEO
Project description:Purpose: The root hair is a model for understanding evolution of individual cell differentiation programs in plants. We compare the expression of the genes that participate in root hair development between Arabidopsis and other vascular plants to assess the conservation/diversification of the root hair development programs in vascular plants. Methods: We used RNA-Seq, in triplicates, to measure the genome-wide transcription activity of the root-hair cells isolated by Fluorescence-activated cell sorting (FACS) in Arabidopsis (COBL9::GFP transgeneic line, AtRH) and rice (EXPA30::GFP transgenic line, OsRH). We also generated RNA-Seq data, in triplicates, on the Arabidopsis rhd6 WER::GFP and WT WER::GFP by FACS to identify the RHD6-regulating root hair morphogenesis genes (AtRHM). For Arabidopsis, rice, tomato, soybean, cucumber and maize, we used RNA-seq, in triplicates, to measure genome-wide transcription activity of root hair cells filtered by sieves after stirred in liquid nitrogen (HAIR genes). Each sample was trimmed to retain high-quality reads, mapped to the reference genome by TopHat, and quantified by Cufflinks. The number of raw reads of Arabidopsis rhd6 WER::GFP and WT WER::GFP sample was counted by HTSeq and analyzed by edgeR to identify the differentially expressed genes. Results: We defined the root-hair transcriptome in diverse vascular plant species and analyzed the relative conservation/divergence in the expression of a large set of gene families.
2017-05-11 | GSE85516 | GEO
Project description:Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restricted by the formation of a suberized exodermis and/or lignified sclerenchyma in the outer part of the root. To characterize reorganization of primary carbon metabolism in rice roots during the ROL barrier formation, we obtained the profiles of polar metabolites and the profiles of fatty acids of different zones of rice roots from plants growing in stagnant (anaerobic) and in well aerated medium. Biochemical data are combined with the results of microarray analysis.
2014-02-18 | GSE52128 | GEO
Project description:Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by genetics and functional genomics approaches. Nevertheless these approaches are impaired by gene function redundancy and mutant lethality. To overcome these limitations, genome-wide transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study we aimed to identify the genes speciffically expressed in developing crown root primordia in comparison with adjacent cortex tissue of stem at three different developmental stages before emergence from the stem. For this, we used Laser Capture Microdissection to collect crown root primordia in the stem base of 8-day-old rice seedlings. Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .
2020-08-26 | GSE133593 | GEO
Project description:Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restricted by the formation of a suberized exodermis and/or lignified sclerenchyma in the outer part of the root. To characterize reorganization of primary carbon metabolism in rice roots during the ROL barrier formation, we obtained the profiles of polar metabolites and the profiles of fatty acids of different zones of rice roots from plants growing in stagnant (anaerobic) and in well aerated medium. Biochemical data are combined with the results of microarray analysis. Nine days after germination, the seedlings were transferred to well aerated nutrient solution or stagnant deoxygenated nutrient solution. Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen, <0.5 mg lM-bM-^@M-^S1) prior to use by flushing with N2 gas. After 14 d (23 d old), adventitious roots, 100-150 mm long, were harvested from rice plants grown either in aerated or stagnant conditions and RNA was extracted from 10 mm segments from the regions 0-10 mm, 10-20 mm and 20-30 mm from the root apex have been cut with sterile razor blade and collected and processed separately. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturerM-bM-^@M-^Ys instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (825 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.
2014-02-18 | E-GEOD-52128 | biostudies-arrayexpress
Project description:Diversification of Root Hair Development Genes in Vascular Plants
| PRJNA338767 | ENA
Project description:Root hairs are an extensive structure of root epidermal cells and are critical for nutrient acquisition, soil anchorage, and environ- mental interactions in sessile plants. The phytohormone ethylene (ET) promotes root hair growth and also mediates the effects of different signals that stimulate hair cell development. However, the molecular basis of ET-induced root hair growth remains poorly understood. Here, we show that ET-activated transcription factor ETHYLENE-INSENSITIVE 3 (EIN3) physically interacts with ROOT HAIR DEFECTIVE 6 (RHD6), a well-documented positive regulator of hair cells, and that the two factors directly coactivate the hair length-determining gene RHD6-LIKE 4 (RSL4) to promote root hair elongation. Transcriptome analysis further revealed the parallel roles of the regulator pairs EIN3/EIL1 (EIN3-LIKE 1) and RHD6/ RSL1 (RHD6-LIKE 1). EIN3/EIL1 and RHD6/RSL1 coordinately en- hance root hair initiation by selectively regulating a subset of core root hair (H) genes. Thus, our work reveals a key transcriptional complex consisting of EIN3/EIL1 and RHD6/RSL1 in the control of root hair initiation and elongation, and provides a molecular framework for the integration of environmental signals and in- trinsic regulators in modulating plant organ development.
2017-12-12 | GSE107699 | GEO
Project description:Cyanide is stoichiometrically produced as a co-product of the ethylene biosynthesis pathway, and it is detoxified by the b-cyanoalanine synthase enzyme. The molecular and phenotypical analysis of T-DNA insertional mutants of the mitochondrial b-cyanoalanine synthase CYS-C1 suggests that discrete accumulation of cyanide is not toxic for the plant and does not alter mitochondrial respiration rates, but does act as a strong inhibitor of root hair development. The cys-c1 null allele is defective in root hair formation and accumulates cyanide in root tissues. The root hair defect is phenocopied in wild type plants by the exogenous addition of cyanide to the growth medium and is reversed by the addition of hydroxocobalamin. Hydroxocobalamin not only recovers the root phenotype of the mutant, but also the formation of ROS at the initial step of the root hair tip. Transcriptional profile analysis of the cys-c1 mutant reveals that cyanide accumulation acts as a repressor signal for several genes encoding enzymes involved in cell wall rebuilding and the formation of the root hair tip, as well as genes involved in ethylene signaling and metabolism. Our results demonstrate that mitochondrial b-cyanoalanine synthase activity is essential to maintain a low level of cyanide for proper root hair development.
2010-10-01 | GSE19242 | GEO