eQTL analysis - Extracting genotype information of recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays

In order to identify eQTL in developing seeds of Arabidopsis thaliana 116 Arabidopsis thaliana recombinant inbred lines (C24/Col 0 and Col 0/C24, Törjék et al. 2006) were analysed. Expression data of 116 recombinant inbred lines (C24/Col 0 and Col 0/C24) that were established for developing seeds of the same stage (10-11 days after flower opening) provided the basis for an eQTL analysis. For each line one biological replicate was evaluated. The data were also used to develop a sequence feature polymorphism map. A sequence-based approach identified features on the array that showed sequence polymorphisms between A. thaliana accessions Col 0 and C24. Hybridisation intensities were retrieved for all probe sets consisting of one or several probes that were polymorphic in C24 (VM probes) and at least three probes that revealed perfect matches to the Col 0 and C24 genomes (IM probes). The mean hybridisation intensity of all IM probes of a particular probe set was divided by that of each VM probe. For each of the polymorphic probes the resulting ratios of all RILs were compiled and sorted in ascending order before they were subjected to a sliding window analysis in order to identify SFP markers. The genotypes of the recombinant inbred lines were determined with the SFP markers and a linkage map of the Col 0/C24 and C24/Col 0 recombinant inbred populations was generated. Data for the parental lines Col-0 and C24 are also available (GSE94762).