Synthetic view of the different transcriptome approaches used to refine abdominal fatness QTL on GGA5. (a) Correlation and differential expression analysis revealed 660 gene mRNA levels related to abdominal fat values (P < 0.05 at the gene level). (b) Expression QTL analysis performed on 11213 genes detected 285 genes for which mRNA levels were regulated by an eQTL which colocalized with the GGA5 AF QTL confidence interval (CI). Venn diagram shows that 46 gene mRNA levels were correlated with AF value and regulated by an eQTL colocalized with the AF QTL confidence interval. (1) First approach: QTL analysis was performed on different animal subgroups identified by double HCA carried out with the 45 animals and the 660 gene mRNA levels. (2) Second approach: we performed 46 new QTL analyses for residual abdominal fat values conditioned by each of the 46 gene mRNA levels. We thus identified 12 genes for which AF values conditioned by their mRNA level did not allow detection of residual AF QTL (p > 0.1), 5 of which were validated by qRT-PCR methodology. A multivariate analysis was then carried out combining a synthetic variable for the 5 gene mRNA levels and the AF trait to refine the QTL region of interest. (3) Third approach: We used the 5 gene mRNA levels to predict the Q/q allele at the causative mutation for each recombinant by discriminate analysis (DA) or logistic regression (LR). Supplementary marker genotyping localized in the AF QTL confidence interval made it possible to define the most probable AF confidence interval QTL. Aims for each approach are indicated in bold.