TABLE 1

Parameters for default and alternative simulated populations

Default population
    Effective population size100
    No. of generations of random mating since QTL mutation occurred100
    No. of markers genotyped10
    No. of alleles per marker in founder population2
    Initial marker/QTL allele frequencies in founder population0.5/0.005
    Distance (cM) between adjacent markers1, 0.5, 0.25
    Position of QTLHalfway between markers 5 and 6
    Additive effect of QTL allele mutation1
    Residual standard deviation1
    No. of individuals (records) in final generation100
Two-breed cross
    No. of generations of random mating following the initial cross1, 5, 10, 20, 100
    Initial marker/QTL allele frequencies in founder population
        Breed 10.5/0.1, 0.9
        Breed 20.5/0.9, 0.1
    Distance (cM) between adjacent markers1
Noncentral QTL position
    Distance (cM) between adjacent markers1
    Position of QTLHalfway between markers 3 and 4
Random founder allele frequencies
    Initial marker/QTL allele frequencies in founder population0.2–0.8/0.005
    Distance (cM) between adjacent markers1
Worst-case scenario
    No. of generations of random mating following the initial cross10
    Initial marker/QTL allele frequencies in founder population
        Breed 10.2–0.8/0.1, 0.9
        Breed 20.2–0.8/0.9, 0.1
    Distance (cM) between adjacent markers1
    Position of QTLHalfway between markers 3 and 4
Alternative effective population size
    Effective population size50, 200
    Distance (cM) between adjacent markers1
Smaller QTL effect
    Distance (cM) between adjacent markers1
    Additive effect of QTL allele mutation0.5
  • Parameters for alternative populations are the same as the default except for those specified here.