k-mer analysis of publicly available resources enables rapid development of an improved KASP marker linked to the H1 resistance locus in potato

High-throughput markers for resistance loci are widely used in potato breeding but often benefit from periodic redevelopment to improve diagnostic performance. Here we re-analysed bulked resequencing data generated by Meade et al. (2020) to redesign a KASP marker for the H1 potato cyst nematode resistance locus. We applied the CoSSA k-mer subtraction approach to sequencing pools generated by Meade et al., extracting H1-associated k-mers and mapping them to the DM reference genome to identify candidate SNPs near the diagnostic 57R region. Two SNPs were converted to KASP assays, of which one produced a modest but statistically significant improvement in classification accuracy relative to the previously published marker when tested across three years of breeding material. This study therefore provides a practical, low‑cost workflow to modernise legacy markers by converting reference‑free k‑mer signals into breeder‑ready assays for potato improvement. This collection provide electronic supplementary material used in the publication: ESM S1: Table: Overview of k-mer data sets from the read archives used and of set operations. ESM S2: Effect of k-mer depth thresholds on genome-wide signal and enrichment at the H1 locus. ESM S3: Table: Effect of k-mer depth cut-offs on signal-to-noise enrichment at the H1 locus. ESM S4: Multi-year KASP marker calls and phenotypic PCN resistance data for validation panel. ESM S5: 99 Candidate SNPs associated with H1 identified on the DM reference genome.