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Title: Transcriptome analysis of hrf1 transformed rice revealed crosstalk between disease resistance and drought tolerance mediated by Harpin      
dateReleased:
12-29-2013
description:
Harpin proteins from Gram-negative plant pathogenic bacteria can activate distinct signaling pathways and cause multiple effects in plants. In this document, we observed the transcriptome profile in transgenic NJH12 and wide type R109 using a customized 57 k rice cDNA microarray and found 225 differentially expressed transcripts related to the responses to biotic and abiotic stresses, including programmed cell death (PCD), defense responses associated with the recognition of pathogen-derived elicitors secondary metabolite biosynthesis, and defense signalling pathways mediated by abscisic acid (ABA), reactive oxygen species (ROS), nitric oxide (NO), polyamines (PAs) and Ca2+, suggesting that the disease resistance and drought tolerance mediated by Harpin protein in hrf1-expressing NJH12 rice has a crosstalk through several signaling pathways. The homozygous T3 NJH12 line is a transgenic rice line generated by transforming rice cultivar R109 with hrf1-containing pBMH9 using Agrobacterium-mediated transformation (Shao et al., 2008). Three T3 progeny of the transgenic NJH12 used in this study were grown in a sterile incubator at 28 ℃ in the greenhouse with a 16 h light/8 h dark cycle. Rice leaves were collected at the four-leaf stage and stored in liquid nitrogen prior to RNA extraction. Wild-type rice R109 was used as the negative control. The experiments for each transgenic line and wild type were repeated three times by three independently grown sets of plants for preparing RNA samples used for independent hybridization to the microarrays. Total RNA was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD). The RNA quality was assessed by formaldehyde agarose gel electrophoresis and concentration was quantitated by spectrophotometric analysis. Total RNA was kept at −80 ℃ and sent to the Affymetrix core facility, where quality-control analysis was carried out before cDNA synthesis from the mRNA, labeling (through synthesis of cRNA with incorporation of biotinylated ribonucleotide analogs), and hybridization to the GeneChip Rice Genome Array (Affymetrix). This chip contains 57, 381 probe sets to query 51, 279 transcripts, which was designed based on the 59, 712 gene predictions of TIGR’s osa1 version 2.0 release. The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix). The results were quantified and normalized using MicroArray Suite 5.0 (GCOS1.4) software (Affymetrix). The gene annotation and pathway identification were performed according to the method described by Shi et al. (2006) and Miao et al. (2010b).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-36661
refinement:
raw
alternateIdentifiers:
36661
keywords:
functional genomics
dateModified:
06-02-2014
availability:
available
types:
gene expression
name:
Oryza sativa
ID:
A-AFFY-126
name:
Affymetrix GeneChip Rice Genome Array [Rice]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-36661/E-GEOD-36661.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-36661/E-GEOD-36661.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=GSE36661
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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