QTL detection using estimated marker-specific variances The marker-specific variances were estimated using the smoothed DHGLM with spatial correlation parameter ρ = 0.9. The dashed horizontal line is the overall variance of SNP effects estimated by GLMM. The peaks higher than this line were detected as QTL, and other small peaks below were suggestive QTL. Simulated QTL are also shown as vertical bars with their heights proportional to the variances they explained. For nice visualization, simulated variances are 1/50 magnified for QT and 1/1500 magnified for BT.