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Series GSE40940 Query DataSets for GSE40940
Status Public on Jan 01, 2014
Title Natural variation of transcriptional networks in Arabidopsis thaliana in response to salt stress
Platform organism Arabidopsis thaliana
Sample organism Arabidopsis
Experiment type Expression profiling by array
Summary Arabidopsis ecotypes of Sha and Ler showed differences in tolerance to salinity stress. A previous study indicated that a premature stop codon resulting in a truncated Response to ABA and Salt 1 (RAS1) protein in Sha contributes to the increased salt tolerance relative to Ler ecotype. Sha exhibited higher germination rates and longer roots on MS plate, presumably due to the decreased ABA sensitivity in Sha. More Sha plants also survived in soil after salt treatment with relatively lower electrolyte leakage when compared to Ler. Transcriptome analysis revealed that expression levels of many genes were changed between Sha and Ler ecotypes and by salt treatments. About 500 transcripts were commonly changed by at least one salinity effect and one ecotype effect, and 171 of them were co-regulated by all four comparisons. Transcripts involved in redox, secondary metabolism, auxin metabolism, photosynthesis, cell wall, and protein synthesis were mainly down-regulated by salinity effects, while transposable element genes, microRNA and antisense sequences, histone superfamily genes, and biotic stress related genes were significantly changed by Sha ecotype effects and only slightly by salinity. Several metabolic pathways such as stress, TCA, hormone/lipid/secondary metabolism, redox, development, and GO terms involved in stress, oxidation, and defense response were enriched by both salinity and ecotype effects. Ninety-five highly inducible genes were identified as candidates of RAS1 target genes and the functions involved hormone metabolism, biotic stress, RNA, DNA synthesis, protein metabolism, cell, and microRNA metabolism. All these results indicated that the Sha ecotype was possibly preconditioned to abiotic stress relative to Ler through regulation of signaling pathways and stress responsive gene expression. These comparative transcriptomic and analytical results also confirm the complexity of ABA responses and salt stress tolerance mechanisms, and they suggest additional targets for improving tolerance.
 
Overall design Ten days old seedlings of two Arabidopsis ecotypes, Sha and Ler, were treated with 100 mM NaCl on MS plate. Plant materials were collected for RNA extraction at 4th days after treatments.
 
Contributor(s) Chan Z
Citation(s) 23894403
Submission date Sep 18, 2012
Last update date Apr 19, 2017
Contact name Zhulong Chan
E-mail(s) zlchan@mail.hzau.edu.cn
Organization name Huazhong Agricultural University
Department College of Horticulture and Forestry Sciences
Street address No. 1, Shizishan St, Nanhu
City Wuhan
State/province Hubei Province
ZIP/Postal code 430070
Country China
 
Platforms (1)
GPL9020 Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Feature Number version)
Samples (8)
GSM1005446 Ler-control_rep1
GSM1005447 Ler-control_rep2
GSM1005448 Ler-salt_rep1
Relations
BioProject PRJNA175411

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
GSE40940_RAW.tar 22.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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