Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comprehensive gene expression profiling of the rice root system based on developmental stages and tissue types

ABSTRACT: The root system is a crucial determinant of plant growth potential because of its important functions, e.g., acquisition of water and nutrients, structural support, and interaction with symbiotic organisms. Elucidating the molecular mechanisms of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants including rice. As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray analysis approach. We performed comprehensive microarray analysis of a rice crown root using laser microdissection and collected a total of 13 samples (3 replicates for each sample except for one sample, 38 total microarray data) representing 8 different developmental stages along the longitudinal axis and 3 distinct tissue-types along the radial axis at 2 different developmental stages. The 8 developmental stages represent root cap, division zone, elongation zone and maturation zone_I, II, III, IV and V. The 3 tissue-types represent epidermis/exodermis/sclerenchyma, cortex, and endodermis/pericycle/stele. In the maturation zone_V, the cortex consisted largely of aerenchyma (non-living cells) and was not used for the microarray analysis.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Yutaka Sato

PROVIDER: E-GEOD-30136 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions.

Takehisa Hinako H Sato Yutaka Y Igarashi Motoko M Abiko Tomomi T Antonio Baltazar A BA Kamatsuki Kaori K Minami Hiroshi H Namiki Nobukazu N Inukai Yoshiaki Y Nakazono Mikio M Nagamura Yoshiaki Y

The Plant journal : for cell and molecular biology 20111025 1

The root system is a crucial determinant of plant growth potential because of its important functions, e.g. uptake of water and nutrients, structural support and interaction with symbiotic organisms. Elucidating the molecular mechanism of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants, including rice (Oryza sativa). As an initial step towards developing a comprehensive understanding of the root system, we performed a large-sca ...[more]

PMID: 21895812

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Project description:Internal aeration is crucial for root growth in waterlogged soil. A barrier to radial oxygen loss (ROL) can enhance long- distance oxygen transport via the aerenchyma to the root tip; a higher oxygen concentration at the apex enables root growth into anoxic soil. The ROL barrier is formed within the outer part of roots (OPR). Suberin and/or lignin depos- ited in cell walls are thought to contribute to the barrier, but it is unclear which compound is the main constituent. This study describes gene expression profiles during ROL barrier formation in rice roots to determine the relative responses of suberin and/or lignin biosyntheses for the barrier. OPR tissues were isolated by laser microdissection and their transcripts were analysed by microarray. A total of 128 genes were significantly up- or downregulated in the OPR during the barrier formation. Genes associated with suberin biosynthesis were strongly upregulated, whereas genes associated with lignin biosynthesis were not. By an ab initio analysis of the promoters of the upregulated genes, the putative cis-elements that could be associated with transcription factors, WRKY, AP2/ERF, NAC, bZIP, MYB, CBT/DREB, and MADS, were elucidated. They were particularly associated with the expression of transcrip- tion factor genes containing WRKY, AP2, and MYB domains. A semiquantitative reverse-transcription PCR analysis of genes associated with suberin biosynthesis (WRKY, CYP, and GPAT) confirmed that they were highly expressed during ROL barrier formation. Overall, these results suggest that suberin is a major constituent of the ROL barrier in roots of rice. 23-d-old plants were either continued in aerated solution or transplanted into N2-flushed or stagnant deoxygenated solution for 9 h. After treating the roots of plants in aerated, stagnant, or N2-flushed conditions for 9h, the basal parts (12.5 -22.5mm below the root - shoot junction) of the adventitious roots were collected. Cells in OPR (including exodermis and sclerenchyma) were isolated using laser microdissection. RNA extracted from the isolated OPR was analysed with a 44k rice oligo-DNA microarray. 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 (10 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.

Dataset Information

Comprehensive gene expression profiling of the rice root system based on developmental stages and tissue types

Publications

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions.

Similar Datasets

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