Linkage analysis on simulated expression phenotypes. Results from Haley-Knott regression for the six models in Figure 1A. In all plots the gene whose expression QTLs are mapped, is represented with a filled circle. The number inside a circle indicates the number of F2 datasets of the total 400 in which the gene is detected as a QTL for the trait being studied. For instance the leftmost plot of model 1, with p = 1, shows that when mapping QTLs for the expression level of gene 1, we detected gene 1 itself in 116 of 400 F2 populations, gene 2 and gene 3 were detected in 4 and 20 F2 populations, respectively. Some false positives are seen when a QTL is reported in the position of a gene downstream of the gene whose expression is being studied.