Figure 3.

Gene and map based models for the putative modes of action of eQTLs and trait QTLs.A. Putative gene-based transcriptional network explaining the relationship of trans-acting eQTLs (transcription factors, TFs) and cis-eQTLs (in target genes) observed at the corresponding trait QTLs. In this model, cis-trans and trans-trans interactions may be possible at the gene and protein levels. B. Map-based model showing the putative interactions of QTLs for wood basic density. In this model, trans-acting eQTLs on LG4 and LG10 (white bars) underlie the wood basic density QTLs observed on these linkage groups, while genes with cis-acting eQTLs on LG8 and 9 (black bars) underlie QTLs detected on the same linkage groups and share trans-eQTLs on LG4 and LG10. The cis-trans interaction (at the gene level) between these two sets of QTLs putatively underlie the detectable epistatic interaction of the wood density QTLs on linkage groups 8 and 10 (Additional file 4 Figure S2).