Marker-assisted selection (MAS) is becoming increasingly common in commercial potato breeding programmes and can provide information to breeders on potential resistance to diseases and pests early in the breeding cycle when phenotypic screens are impractical. In recent years, a wealth of information on molecular markers for genes involved in resistance to biotic stresses of potato has been revealed. However, markers come in many different forms and ideally a breeding programme would routinely perform annual genotyping on a single unified platform. In this study, we present an approach to consolidate various types of molecular markers to a single SNP-based platform using whole-genome sequencing of carefully constructed pools of DNA using, as examples, molecular markers for the H1 nematode and R2 blight resistance genes. The approach led to the identification of a number of candidate nucleotide polymorphisms which allowed successful design and deployment of kompetitive allele-specific PCR (KASP) assays. We further show how the sequence data generated can be used to aid design of KASP assays for diagnostic SNPs for other traits mined from the literature.