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Series GSE57770 Query DataSets for GSE57770
Status Public on Sep 30, 2014
Title Root transcriptome comparison between grapevines Cabernet Sauvignon, 140 Ruggeri and K51-40 (+/- salt stress)
Platform organism Vitis vinifera
Sample organisms Vitis vinifera; Vitis cinerea var. helleri x Vitis rupestris; Vitis x champinii x Vitis riparia
Experiment type Expression profiling by array
Summary Salt tolerance in grapevine is associated with the exclusion of chloride ions (Cl–) from the shoot. The rate-limiting step for this process has been identified as the passage of Cl– between the root symplast and the xylem apoplast through membrane integral proteins. To identify candidate genes for these proteins we used a custom microarray to compare the root transcriptomes of three grapevine varieties (Vitis spp.) that differ in their capacity to exclude Cl– from shoots. When challenged with 50 mM Cl– there were transcriptional responses that differed across the rootstocks 140 Ruggeri (a good Cl– excluder) and K51-40 (a poor Cl– excluder), and Cabernet Sauvignon (an intermediate Cl– excluder and Vitis vinifera control). The magnitude of these salt-induced changes correlated with the amount of Cl– accumulated in shoots. Abiotic-stress responsive transcripts (e.g. heat shock proteins) were induced in 140 Ruggeri. Respiratory transcripts were repressed in Cabernet Sauvignon. Expression of hypersensitive response and ROS scavenging transcripts were altered in the sensitive K51-40. Despite these differences, no obvious candidate Cl– transporters were identified from the salt treatment. In contrast, under control conditions where differences in shoot Cl– exclusion between rootstocks were still significant, we identified a number of genes encoding putative ion channels including VvSLAH3, VvALMT1, and possible regulators of these proteins such as VvSnRK2.6 and calcium dependent protein kinases (CDPK) as being differentially expressed between rootstocks. Members of the low affinity nitrate transporter (NRT1), and chloride channel (CLC) families were also identified. We propose these as useful candidates for further study within breeding programs aimed at improving plant salt tolerance in grapevine and other crops.
 
Overall design Comparative: genotype versus genotype (control); and control (0 mM Cl) versus salt (50 mM Cl). Rooted leaves were grown as described by Gong et. al. (2010) (Journal of Experimental Botany). After 2 weeks of hydroponic growth, plants were exposed to 0 mM or 50 mM chloride stress for 4 days. Three biological replicates were used for 140 Ruggeri. Four biological replicates were used for Cabernet Sauvignon. Four biological replicates were used for K51-40. Each biological replicate consisted of total roots from four individual plants pooled together.
 
Contributor(s) Henderson SW, Baumann U, Gilliham M
Citation(s) 25344057
Submission date May 19, 2014
Last update date Aug 16, 2019
Contact name Sam Henderson
E-mail(s) sam.henderson@adelaide.edu.au
Organization name University of Adeladie
Street address Hartley Grove
City Urrbrae
State/province South Australia
ZIP/Postal code 5064
Country Australia
 
Platforms (1)
GPL18706 Agilent-036223 Vitis_vinifera.IGGP_12x.2_vs20110825
Samples (22)
GSM1388329 CabernetSauvignon_Root_Control_1
GSM1388330 CabernetSauvignon_Root_Control_2
GSM1388331 CabernetSauvignon_Root_Control_3
Relations
BioProject PRJNA248107

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57770_RAW.tar 66.1 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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