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. 

Brito et al. BMC Genetics 2011 12:80 doi:10.1186/147121561280 