TABLE 3

Detection and characterization of Mendelian QTL

Simulation detailsImprinting inferred
No. males/females F1QTL effecta (frequency)PowerbMaternalPaternal
Mend.Mat.Pat.FMend c Fred d BotheFMend c Fred d Bothe
20/80No QTL0.050.050.050.030.050.030.030.050.03
A 0.75 (1.0/0.0)1.01.01.00.050.000.000.050.000.00
A 0.50 (1.0/0.0)1.01.01.00.060.010.000.060.010.00
A 0.25 (1.0/0.0)0.850.640.620.070.280.060.060.270.05
D 0.75 (1.0/0.0)1.01.01.00.050.00.000.050.000.00
D 0.50 (1.0/0.0)1.00.991.00.050.010.000.050.000.00
D 0.25 (1.0/0.0)0.960.610.600.060.150.040.060.130.04
A 0.75 (0.8/0.2)0.990.940.910.110.110.060.080.070.02
A 0.50 (0.8/0.2)0.910.720.710.070.240.060.080.220.06
A 0.25 (0.8/0.2)0.370.250.380.050.190.050.060.220.06
D 0.75 (0.8/0.2)0.980.880.870.090.090.030.100.060.02
D 0.50 (0.8/0.2)0.90.660.670.080.190.060.080.170.05
D 0.25 (0.8/0.2)0.390.240.250.070.170.060.070.190.06
2/80No QTL0.050.050.040.030.040.030.030.040.03
A 0.50 (1.0/0.0)1.00.990.990.060.010.000.050.010.00
A 0.75 (0.8/0.2)0.920.940.820.330.170.130.280.050.03
A 0.50 (0.8/0.2)0.830.770.710.180.240.130.210.170.10
A 0.25 (0.8/0.2)0.400.280.320.070.210.070.090.240.09
D 0.75 (0.8/0.2)0.890.820.770.350.150.120.320.070.04
D 0.50 (0.8/0.2)0.830.650.670.190.190.120.210.120.06
D 0.25 (0.8/0.2)0.470.300.320.090.200.080.090.200.07

QTL were simulated under a Mendelian model and analyzed under Mendelian (Mend.) and imprinting [maternal/paternal (Mat./Pat.)] models for 400 F2 animals with different designs, QTL effects, and allele frequencies.

  • a A, additive QTL; D, dominant QTL with a = d (frequency of positive QTL allele in F0).

  • b Proportion of replicates significant at the 5% chromosome-wide level against the H0 of no QTL.

  • c Proportion of replicates significant at the 5% chromosome-wide level and for which a full model explains significantly more variance (P < 0.05) than a Mendelian QTL at the position of the best QTL under the respective model.

  • d Proportion of replicates significant at the 5% chromosome-wide level and for which a full model does not explain significantly more variance (P < 0.05) than a QTL with a single parental effect at the position of the best imprinted QTL.

  • e Proportion of replicates where both tests of full vs. Mendelian (FMend) and reduced vs. full (Fred) indicate imprinting.