Table 1 Number of QTL and their contribution to the additive genetic variance VA (in percent) for all QTL segregating in the population and those detected by GWAS with the full sequence as a function of their gene frequencies (rare: q ≤ 0.05; common: q > 0.05) and absolute effects on the quantitative trait (a, in pSDs)
FrequencyEffect a (pSDs)Number%VA
All QTLGWASRHMGWAS + RHMAll QTLGWASRHMGWAS + RHM
Rare, q ≤ 0.050–0.0399,801141271380.20.00.00.0
0.03–0.1413,530018183.60.00.00.0
0.14–0.282,5040114.90.00.00.0
0.28–0.567582135.10.10.00.2
>0.56714341.90.80.70.8
Common, q > 0.050–0.0324,6375238641.20.00.00.0
0.03–0.142,7271451419.50.20.10.2
0.14–0.2855573267630.78.63.68.9
0.28–0.5612792679524.921.818.822.7
>0.56121212127.97.97.97.9
144,722263298425100.039.431.140.6
  • The results correspond to the six whole genomes simulated under the scenario with ρ = 0.5. The threshold value for detection is a probability of α = 10−8 both for GWAS and for RHM.