Table 2 Simulation results of mapping epistatic QTL using the complete genotyping and selective genotyping 100/200 design in the F2 population with 15-cM marker map
Without epistasisaWith epistasisb
QAQBQAQB
MethodPowerPosi.a1 = 3d1 = 1PowerPosi.a2 = 1PowerPosi.a1 = 3d1 = 1PowerPosi.a2 = 1iaa = 2
Complete genotyping
100/100c0.76553.2 (18.1)2.98 (0.86)0.92 (1.48)0.09980.5 (43.3)1.05 (1.27)0.90353.2 (18.0)2.99 (0.85)0.94 (1.47)0.19683.3 (37.8)0.96 (1.11)1.80 (1.73)
200/2000.97852.0 (9.2)2.93 (0.58)0.99 (0.91)0.23784.4 (36.1)1.12 (0.79)0.99951.9 (9.1)2.94 (0.57)1.00 (0.89)0.50788.3 (25.7)1.03 (0.70)1.95 (1.06)
Selective genotyping
PFB M.d0.96952.0 (10.1)2.94 (0.61)1.06 (1.00)0.19682.8 (36.5)1.14 (0.86)0.99451.9 (10.0)2.95 (0.60)1.01 (0.99)0.38586.9 (29.5)1.03 (0.77)1.87 (1.25)
Truc. M.e0.97252.0 (10.6)3.07 (0.72)1.10 (1.11)0.21682.5 (37.3)1.19 (0.95)0.99552.1 (10.5)3.15 (0.75)0.98 (1.11)0.38185.4 (31.5)1.05 (0.90)1.99 (1.52)
Prop. M.f0.97152.1 (10.3)3.08 (0.68)1.12 (1.09)0.23181.9 (36.7)1.18 (0.93)0.99552.1 (10.3)3.12 (0.69)1.06 (1.07)0.49886.7 (31.6)0.98 (0.85)2.10 (1.42)
  • a With epistasis ignored.

  • b With epistasis considered.

  • c The total 100 sampled individuals are genotyping.

  • d The population frequency-based method (see text).

  • e The truncated model.

  • f The proposed method. Numbers in the parentheses are standard deviations. The critical values for claiming significance are 9.18 and 12.34 for 1 and 2 degrees of freedom for the test. Two unlinked QTL, QA and QB, are simulated on the chromosomes with 11 15-cM equally spaced markers. QA is placed at 52 cM with additive effect 3 and dominance effect 1 (a1 = 3, d1 = 1,VA/VG = 76%). QB is placed at 93 cM with additive effect 1 (a2 = 1, VB/VG = 8%). The mean is zero, and the additive by additive epistatic effect is 2 (μ = 0, iaa = 2, Vi/VG = 16%). The heritability is 0.2 (h2 = 0.2, σ2 = 25). The simulated replicates are 1000.