Table 1.
Parameters of the simulation process
| Population structure | POP1/POP2 |
|---|---|
| Step 1: Historical generations (HG) | |
| Number of generations(size) - phase 1 | 1000(1000) |
| Number of generations(size) - phase 2 | 1020(200) |
| Step 2: Expanded generations (EG) | |
| Number of founder males from HG | 100 |
| Number of founder females from HG | 100 |
| Number of generations | 8/6 |
| Number of offspring per dam | 5 |
| Step 3: Recent generations | |
| Number of founder males from EG | 640/160 |
| Number of founder females from EG | 32000/8000 |
| Number of generations | 10 |
| Number of offspring per dam | 1 |
| Ratio of male | 50% |
| Mating system | Random |
| Replacement ratio for males | 60% |
| Replacement ratio for females | 20% |
| Selection/culling | EBV |
| BV estimation method | BLUP animal model |
| Ratio of missing sire and dam | 5% |
| Heritability of the trait | 10%, 25%, or 40% |
| Phenotypic variance | 1.0 |
| Genome | |
| Number of chromosomes | 29 |
| Total length | 2333 cM |
| Number of markers | 40000/800000 |
| Marker distribution | Evenly spaced |
| Number of QTL | 750 |
| QTL distribution | Random |
| MAF for markers | 0.1 |
| MAF for QTL | 0.1 |
| Additive allelic effects for markers | Neutral |
| Additive allelic effects for QTL | Gamma distribution (shape = 0.40) |
| Rate of missing marker genotypes | 0.01 |
| Rate of marker genotyping error | 0.005 |
| Rate of recurrent mutation | 0.0001 |
POP1: population 1; POP2: population 2; EBV: estimated breeding value; BV: breeding value; QTL: quantitative trait loci; MAF: minor allele frequency.
The whole simulation process was repeated 10 times.