Whole-genome sequencing (WGS) of pools of individuals (Pool-Seq) approach provides a cost-effective method for genome-wide association studies (GWAS) alternative to sequencing of individuals that is very expensive. Pool-Seq is being increasingly used in population genomic studies in both model and non-model organisms. In this paper, the ability of Pool-Seq approach to recover known GWAS signals was evaluated. Existing GWAS data for 2,112 animals with 729K SNPs were obtained and pooled to simulate data obtained from a pooled WGS approach. Traditional SNP association was compared with the absolute allele frequency difference (dAF) results; the ability of dAF scans to recover signals obtained from SNP association was tested in three different traits (with large and moderate gene effects).