Method | unequal QTL variance | equal QTL variance |
|---|
| Â | low nQTL | int. nQTL | high nQTL | low nQTL | int. nQTL | high nQTL |
|---|
Standard | 0.80 (0.007) | 0.67 (0.006) | 0.57 (0.007) | 0.69 (0.005) | 0.62 (0.006) | 0.57 (0.006) |
h2 = 0.25 | 0.68 (0.011) | 0.52 (0.006) | 0.56 (0.008) | 0.57 (0.004) | 0.51 (0.005) | 0.53 (0.006) |
MAF>0.10 | 0.77 (0.008) | 0.69 (0.006) | 0.64 (0.007) | 0.67 (0.006) | 0.66 (0.005) | 0.61 (0.004) |
- The simulated number of QTL was low (low nQTL), intermediate (int. nQTL) or high (high nQTL). The simulated variance of every tenth QTL was 81 times larger than variance of remaining QTL (unequal QTL variance) or equal for all QTL (equal QTL variance). The rows of the table correspond to the standard situation (h2 = 0.5, size of training population = 500 individuals, all markers included), the situation with h2 = 0.25, and the situation where markers with MAF < 0.10 were excluded from the data. Method BM was used to calculate the. The prior number of QTL was 35 QTL in the scenarios with a low number of QTL, 172 QTL in the scenarios with an intermediate number of QTL, and 343 QTL in the scenarios with a high number of QTL. The prior for QTL variance was the ratio of the total genetic variance (Table 2) and the number of QTL. The averages and standard deviations were calculated using 60 replicated simulations
