Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-5939 - Transcription profiling of wheat - expression level polymorphism study 36 genotypes 2 biological replicates from SB location

Status
Released on 14 June 2008, last updated on 27 March 2012
Organism
Triticum aestivum
Samples (72)
Array (1)
Protocols (6)
Description
The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 36 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material in location 2 identified 10,280 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. Of these 1,455 were identified in the point location as well. A sub-set of 542 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Experiment Overall Design: 36 genotypes of mapping population RL4452 x AC Domain with 2 biological replicates per genotype. Grown in the field in a lattice design at SB location
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci. Mark C Jordan, Daryl J Somers, Travis W Banks. Plant Biotechnol J 5(3):442-53 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Links