SNPscan breeder is a software that enables the simulation of breeding programs using simulated individual whole genome data, different genetic architectures of a trait of interest, different mating designs and different selection criteria, i.e. pheno-types, breeding values from progeny tests, marker-assisted selection (MAS) and genomic selection (GS). The impact of breeding population size, mating design, selection intensity, genetic architecture, heritability and selection criteria on genetic gains, kinship, inbreeding and genetic diversity can be evaluated to optimize the breeding program. A special feature is the possibility for post-hoc analysis of different strategies to identify causal SNPs and allele effects within the frame of genome-wide association studies (GWAS). The proportion of true and false positive SNPs and the correlation of estimated and true allelic effects can be measured and the overall impact of their use for MAS on the success of the breeding program can be tested.
