E-TABM-62 - Transcription profiling of 148 Arabidopsis recombinant inbred lines treated with Silwet solution to develop genetic markers and derive high-density haplotypes

Status
Released on 10 January 2007, last updated on 2 May 2014
Organism
Arabidopsis thaliana
Samples (298)
Array (1)
Protocols (9)
Description
The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We surveyed recombinant inbred lines (RILs) from a population derived from a cross of inbred Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) in order to map e-QTLs controlling ELPs. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 28 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for 148 RILs, plus replicated Bay-0 and Sha control samples grown at the same time as the RILs. These GeneChips were used to develop genetic markers and derive high-density haplotypes for the RILs
Experiment types
transcription profiling by array, compound treatment, strain or line
Contacts
Dina St. Clair <dastclair@ucdavis.edu>, Alexander Kozik, Daniel J. Kliebenstein, Dina A. St Clair, Hans van Leeuwen, Marilyn A.L. West, R W. Doerge, Richard W. Michelmore
Citation
High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Marilyn A.L. West; Hans van Leeuwen; Alexander Kozik; Daniel J. Kliebenstein; R. W. Doerge; Dina A. St.Clair; Richard W. Michelmore. Genome Res 16(6):787-95 (2006), Europe PMC 16702412
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-TABM-62.idf.txt
Sample and data relationshipE-TABM-62.sdrf.txt
Processed data (1)E-TABM-62.processed.1.zip
Array designA-AFFY-2.adf.txt
Links