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Title: Microarray analysis of laser-microdissected tissues indicates the biosynthesis of suberin in the outer part of roots during formation of a barrier to radial oxygen loss in rice (Oryza sativa)      
dateReleased:
06-26-2014
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 manufacturer’s instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (10 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-58804
refinement:
raw
alternateIdentifiers:
58804
keywords:
functional genomics
dateModified:
07-14-2014
availability:
available
types:
gene expression
name:
Oryza sativa
ID:
A-GEOD-6864
name:
Rice 44K
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58804/E-GEOD-58804.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58804/E-GEOD-58804.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58804
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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