Method | Param | Ref simul | QTL effect | Marker density | Sample size | Effective size |
---|
| QTL | 0.25 | 0.5 | | | | | | | |
|
N
e
| 100 | | | | | | 200 | 400 | 400 |
|
N
g
| 50 | | | | | | | | 200 |
|
N
s
| 20 | | | | 20 | 10 | | | |
|
N
p
| 100 | | | | 50 | 50 | | | |
|
dens
| 0.25 | | 0.125 | 0.5 | | | | | |
HaploMax | | 2.018 | 1.431 | 2.138 | 2.134 | 2.496 | 2.774 | 2.493 | 2.840 | 2.054 |
HAPimLDL | | 2.165 | 1.528 | 2.114 | 2.296 | 2.716 | 2.990 | 2.635 | 2.834 | 2.147 |
- Square roots of MSE values (in cM) for both methods, HaploMax and HAPimLDL, under various scenarios; we assumed complete linkage disequilibrium between the QTL and the markers and linkage equilibrium between the markers in the founder population; the haplotype is composed of the QTL and two flanking markers; the true QTL position is 3.35 cM on a 10 cM-long chromosomal region; unspecified parameters are equal to the corresponding parameters in the reference simulation; in this table, QTL denotes the QTL allelic effect value, N
e
is the effective size of the population, N
g
is the number of generations, N
s
is the number of sires, N
p
is the number of progeny per sire and dens is the marker density; each scenario was simulated 500 times