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:10.1186/1471-2156-12-80

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