Table 3 . Detailed description of the single-marker simulation scenarios.

Scenario	Tested parameter	h2	QTL effect	Sample size	MAF	LD	d/|a|	Range of modified parameter	Explanatory notes
1	Sample size	0.2	0.2σA	—	0.3	r2 = 1	0.5	N = 50,000–1,000,000 (14 steps)	Heritability and effect size were reduced to achieve a higher resolution across the entire range of N. True genotypes were compared with genotype probabilities.
2	No. considered generations	0.25	0.5σA	N = 5,000–100,000 (19 steps)	0.3	r2 = 1	0.5	2 sires vs. 3 sires	Genotype probabilities were calculated using a genotyped sire and grandsire only or including an additional great-grandsire in an increasing sample size.
3	Minor allele frequency	0.25	0.5σA	10,000 vs. 100,000	—	r2 = 1	0.5	MAF = 0.025–0.5 (19 steps)	MAF was increased stepwise in two different sample sizes.
4	LD between QTL and marker	0.25	0.5σA	N = 5,000–100,000 (19 steps)	0.3/0.5	—	0.5	r2 = 0.4/0.6/0.8	An increasing sample size was analyzed for three different r2 values and two different MAFs.
5	Variance explained by the QTL	0.25	—	10,000 vs. 100,000	0.3	r2 = 1	1	${\sigma }_{\text{QTL}}^2/{\sigma }_{\text{A}}^2$ = 0.01–0.2 (14 steps)	${\sigma }_{\text{QTL}}^2/{\sigma }_{\text{A}}^2$ was increased stepwise in two different sample sizes.
6	Degree of dominance	0.25	0.5σA	10,000 vs. 100,000	0.3	r2 = 1	—	d/a = 0.05–2 (39 steps)	d/|a| was increased stepwise in two different sample sizes. True genotypes were compared with genotype probabilities within these samples.

For each scenario, the range of the modified parameter is given together with the fixed parameters. The QTL effects are expressed as additive genetic standard deviations (σ_A). MAF and LD stand for minor allele frequency and linkage disequilibrium, respectively. The degree of dominance was calculated as the ratio of dominance effect and absolute additive effect (d/|a|).