When creating a synthetic line, two or more breeds are crossed to produce animals that combine the desired characteristics of the parental populations. In this context, it is relevant to ensure whether the genomic balance among the breeds involved in the initial cross is maintained over several generations. In principle, this balance can be monitored using dense genotypes of individuals from the line. In this study, we report the development and use of monitoring methods in a new synthetic pig line created by three-way crossbreeding between Pietrain x Large White (PLW) sows and Duroc boars. The offspring of this crossbreeding are the first generation of the line (G0). In G1, the proportions of PLW and Duroc were available, allowing the selection of individuals balanced between the two origins. All founders of the line and animals from the first three generations (G0, G1 and G2) were genotyped for ~50K SNPs. To estimate the proportions of Duroc, Large White and Pietrain origins independently, we used a new method that combines genotypes and pedigree data. For each crossbred animal, each of its chromosomal fragments is assigned to one of the three parental breeds. In G2, we obtained the following mean average proportions: 0.50 ± 0.07 from Duroc, 0.24 ± 0.05 from Large White and 0.25 ± 0.05 from Pietrain, which are consistent with the expected proportions. Optimal results are obtained when all ancestors up to purebred founders are genotyped.