Analyses of gene expression of the six candidate genes by qPCR method (A), multiple probe-sets from the microarray (B) and genome-wide interval mapping (C). A. Results of qPCR are presented as fold change of average expression level across all the four mouse strains. Transcript region covered by Taqman probe is marked in the scheme of transcript structure. Error bars represents ± standard error of the mean from 6–9 individual animals. Statistical significance was determined by using ANOVA analysis followed by Tukey post hoc test (*p < 0.05, **p < 0.01, ***p < 0.001). B. Relative inter-strain differences in expression are presented as results from the multiple probe-sets measured by the MBEI method. Each probe was aligned with mRNA sequence and exon structure downloaded from Ensembl or GenBank databases. Image displays signal intensity from an individual array with emphasized mean value. Array probe-sets marked in red were found to be significantly different between the four strains of mice. C. Genome-wide interval multiple mapping for six probe-sets (Atp1a2 – 1455136_at, Kcnj9 – 1450712_at, Gabra2 – 1443865_at, Grm7 – 1459532_at, Gabra1 – 1436889_at, Comt – 1418701_at) in WebQTL (HBP/Rosen Striatum M430V2 (Apr05) PDNN Clean). The likelihood ratio statistics (LRS) score for association of the gene expression with genotype across genome of BXD recombinant strains for each probe-set is represented as coloured trace. Mouse chromosomes are plotted along y-axis, with the exception for chromosome Y. Coloured triangles indicate transcript locations. Cis-regulatory QTLs for Atp1a2 (1455136_at), Kcnj9 (1450712_at), Grm7 (1459532_at), Comt (1418701_at) are marked with black arrows.