TABLE 1.

Parameters for default and alternative simulated populations

Default population
Effective population size	100
No. of generations of random mating since QTL mutation occurred	100
No. of markers genotyped	10
No. of alleles per marker in founder population	2
Initial marker/QTL allele frequencies in founder population	0.5/0.005
Distance (cM) between adjacent markers	1, 0.5, 0.25
Position of QTL	Halfway between markers 5 and 6
Additive effect of QTL allele mutation	1
Residual standard deviation	1
No. of individuals (records) in final generation	100
Two-breed cross
No. of generations of random mating following the initial cross	1, 5, 10, 20, 100
Initial marker/QTL allele frequencies in founder population
Breed 1	0.5/0.1, 0.9
Breed 2	0.5/0.9, 0.1
Distance (cM) between adjacent markers	1
Noncentral QTL position
Distance (cM) between adjacent markers	1
Position of QTL	Halfway between markers 3 and 4
Random founder allele frequencies
Initial marker/QTL allele frequencies in founder population	0.2–0.8/0.005
Distance (cM) between adjacent markers	1
Worst-case scenario
No. of generations of random mating following the initial cross	10
Initial marker/QTL allele frequencies in founder population
Breed 1	0.2–0.8/0.1, 0.9
Breed 2	0.2–0.8/0.9, 0.1
Distance (cM) between adjacent markers	1
Position of QTL	Halfway between markers 3 and 4
Alternative effective population size
Effective population size	50, 200
Distance (cM) between adjacent markers	1
Smaller QTL effect
Distance (cM) between adjacent markers	1
Additive effect of QTL allele mutation	0.5

Parameters for alternative populations are the same as the default except for those specified here.