Phenotype simulation was based on work by Saint-Pierre and colleagues [14]. For each individual, three quantitative traits Yj (j = 1, 2, 3) were simulated. The trait-specific QTL heritabilities (the relative variance of Yj explained by the QTL, h2 j), MAF of the QTL q, and residual correlation between the traits excluding the QTL effect (rEjj) were controlled.
