Table 2.
Simulated QTL genotypes and estimated posterior genotype probabilities in the pilot dataset for map intervals with positive QTL evidence of the 16 mapping parents
| Parent | No. of crosses | No. of progeny | Simulation | Modela | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| UNR | TIBD | LAAM | ||||||||||||
| Position (cM) | Intervals (cM) | Intervals (cM) | Intervals (cM) | |||||||||||
| 30 | 60 | 140 | 28–37 | 58–64 | 134–143 | 25–32 | 57–61 | 136–142 | 26–33 | 58–62 | 138–143 | |||
| 761 | 4 | 83 | 1 | 0 | 1 | 0.3 | 0.6 | 0.5 | 0.9 | 0.1 | 1.0 | 0.7 | 0.1 | 1.0 |
| 766 | 2 | 59 | 0 | 0 | 0 | 0.3 | 0.3 | 0.1 | 0.1 | 0.0 | 0.2 | 0.1 | 0.0 | 0.2 |
| 773 | 8 | 248 | 1 | 0 | 1 | 0.3 | 0.5 | 0.8 | 0.9 | 0.1 | 1.0 | 0.7 | 0.1 | 1.0 |
| 775 | 3 | 145 | 0 | 1 | 1 | 0.3 | 0.8 | 0.7 | 0.1 | 1.0 | 1.0 | 0.1 | 0.9 | 1.0 |
| 822 | 2 | 97 | 1 | 0 | 1 | 0.3 | 0.7 | 0.7 | 0.9 | 0.0 | 1.0 | 0.9 | 0.0 | 1.0 |
| 847 | 4 | 197 | 0 | 0 | 0 | 0.1 | 0.4 | 0.1 | 0.1 | 0.0 | 0.0 | 0.1 | 0.0 | 0.0 |
| 851 | 6 | 230 | 1 | 0 | 0 | 0.8 | 0.3 | 0.1 | 1.0 | 0.0 | 0.0 | 0.9 | 0.0 | 0.0 |
| 853 | 5 | 190 | 1 | 0 | 0 | 0.4 | 0.1 | 0.1 | 0.9 | 0.0 | 0.0 | 0.9 | 0.0 | 0.0 |
| 855 | 4 | 119 | 0 | 0 | 1 | 0.4 | 0.4 | 0.3 | 0.1 | 0.0 | 1.0 | 0.1 | 0.0 | 1.0 |
| 857 | 7 | 283 | 0 | 1 | 1 | 0.2 | 0.8 | 0.9 | 0.1 | 1.0 | 1.0 | 0.1 | 0.9 | 1.0 |
| 859 | 3 | 100 | 1 | 0 | 0 | 0.3 | 0.5 | 0.1 | 0.9 | 0.1 | 0.0 | 0.9 | 0.1 | 0.0 |
| 861 | 3 | 69 | 1 | 0 | 1 | 0.5 | 0.8 | 0.8 | 0.9 | 0.8 | 0.9 | 0.9 | 0.2 | 0.9 |
| 863 | 1 | 40 | 1 | 1 | 0 | 0.7 | 0.8 | 0.1 | 1.0 | 1.0 | 0.0 | 0.9 | 0.9 | 0.0 |
| 865 | 2 | 23 | 0 | 1 | 0 | 0.7 | 0.7 | 0.1 | 0.1 | 1.0 | 0.0 | 0.1 | 0.9 | 0.0 |
| 867 | 2 | 82 | 1 | 0 | 0 | 0.4 | 0.6 | 0.1 | 0.9 | 0.0 | 0.0 | 0.8 | 0.1 | 0.0 |
| 869 | 4 | 179 | 1 | 1 | 0 | 0.8 | 0.8 | 0.1 | 0.9 | 1.0 | 0.0 | 0.9 | 1.0 | 0.0 |
Average 
|
0.44 | 0.39 | 0.18 | 0.08 | 0.08 | 0.04 | 0.11 | 0.06 | 0.05 | |||||
The absolute difference between true (simulated) and estimated QTL genotype is given as the parents’ average
The posterior probabilities pertain to the increasing QTL genotype, denoted “QQ” or “++”. The probabilities for the decreasing QTL genotype, denoted “qq” or “−−” is equal to one minus the printed probability. The probabilities that are smaller than or equal to 0.1 and probabilities that are larger than or equal to 0.9 are bold printed
The map regions with positive QTL evidence are intervals with bins having a 2ln(BF) > 2. These regions are also depicted in Fig. 4
aModel abbreviations: UNR model with unrelated parents (without Ancestral Classes), TIBD model with ancestral allele classes and Threshold sampling approach, LAAM model with ancestral allele classes and Latent Ancestor Allele approach