The development and application of haplotype-specific markers for resistance genes is vital to developing new potato varieties for sustainable production. The best available marker for the RB gene, which confers resistance to many races of the late blight pathogen Phytophthora infestans, is based on the presence/absence of a PCR product and visualized using gel electrophoresis. A similar method is commonly used to test for Ryadg, an extreme resistance gene for potato virus Y (PVY). The performance of these markers was compared with results from detached leaf assays and haplotype analysis in F1 tetraploid populations from the UW-Madison breeding program. Selected tetraploids containing RB and/or Ryadg were crossed with the haploid inducer IVP101, and dihaploids were selected as parents for further breeding based on the genetic marker results. To screen diploid and tetraploid populations more efficiently, we also tested a KASP marker for Ryadg and are developing a new KASP marker for RB. To identify haplotype-specific SNPs for the RB introgression from S. bulbocastanum, we are using a method known as Comparative Subsequence Sets Analysis (CoSSA), which involves set-theoretic operations on k-mers derived from whole genome sequencing.