In pigs, the breeding goal is to improve performance of crossbred animals in commercial farms. The best purebred animals to produce crossbred animals can be selected based on their genomic estimated breeding value (GEBV) for crossbred performance. GEBVs are the result of combining estimated effects of genomic markers, usually single nucleotide polymorphisms (SNPs), with the animal’s genotype. The genome of crossbred animals is a mosaic of genomic regions inherited from the different parental breeds, therefore, this thesis aimed to investigate whether SNP alleles have different effects depending from which parental breed the allele was inherited and study the impact on GEBV of purebred animals for crossbred performance when breed-specific allele effects were taken into consideration. We conclude that when the estimated genetic correlation between the performance of purebred and crossbred animals differed largely per breed of origin, it was better to use models that make a distinction of alleles according to their breed of origin but only for SNPs that are associated to the trait.