Table 2. Comparison of accuracy of genomic selection for QTL with different minor allele frequency when predictions are based on SNP panel genotypes, sequence variant genotypes (all individuals sequenced) or imputed sequence variant genotypes.

	QTL frequency (MAF)
	<1%	<10%	Neutral
SNP panel	0.324	0.786	0.894
All individuals sequenced	0.448	0.817	0.907
Comparing strategies for selection of individuals (50@ × 12 for all strategies)
AHAP	0.338	0.804	0.904
REL	0.341	0.801	0.902
IDPT	0.360	0.805	0.903
Comparison of sequencing strategies
25@ × 24	0.315	0.786	0.898
50@ × 12	0.338	0.804	0.904
75@ × 8	0.339	0.806	0.904
100@ × 6	0.331	0.799	0.904
Effect of increasing sequencing effort
150@ × 8	0.381	0.812	0.905
300@ × 8	0.405	0.815	0.906

Abbreviations: MAF, minor allelic frequency; QTL, quantitative trait loci; SNP, single-nucleotide polymorphism.

Accuracies are the average of 25 replicates.