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Table 1 Parameters of the simulation process

From: Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle

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
  1. POP1: population 1; POP2: population 2; EBV: estimated breeding value; BV: breeding value; QTL: quantitative trait loci; MAF: minor allele frequency.
  2. The whole simulation process was repeated 10 times.