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Title KASP Marker Development for Potato H1 Resistance via Public K-mer Analysis
License Creative Commons Attribution 4.0
Teagasc Department Crops Research
Teagasc Programme Crops, Environment and Land Use
Description Electronic supplementary material (ESM S1-S5) for a study that redeveloped a KASP marker for the H1 potato cyst nematode (PCN) resistance locus in potato. Bulked resequencing data from Meade et al. (2020) were re-analysed with the CoSSA k-mer subtraction approach. H1-associated k-mers were extracted and mapped to the DM potato reference genome, giving 99 candidate SNPs near the diagnostic 57R marker region. Two SNPs were converted to KASP assays and tested on three years of breeding material. One gave a modest but statistically significant improvement in classification accuracy over the previously published marker. The dataset documents a low-cost workflow for turning reference-free k-mer signals from public sequence data into breeder-ready marker assays. It contains: the k-mer datasets and set operations used (S1); the effect of k-mer depth thresholds on genome-wide signal and H1 enrichment (S2, S3); multi-year KASP calls with phenotypic PCN resistance data for the validation panel (S4); and the 99 candidate SNPs (S5).
Language English
Principal Investigator (PI) Stephen Byrne
Principal Investigator (PI) email stephen.byrne@teagasc.ie
Principal Investigator (PI) ORCID http://orcid.org/0000-0002-1179-2272
Data creator(s)
  1. Vexler, L
  2. Milbourne, D.
Geographic coverage Teagasc Oak Park, Carlow, Ireland
Digital Object Identifier (DOI) https://doi.org/10.5281/zenodo.19629845
Citation Vexler, L., Byrne, S., & Milbourne, D. (2026). k-mer analysis of publicly available resources enables rapid development of an improved KASP marker linked to the H1 resistance locus in potato [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.19629845
Landing page https://zenodo.org/records/19629845
Rights notes https://creativecommons.org/licenses/by/4.0/deed.en
Project funders European Union Horizon Europe, IPMorama project ("Integrating breeding for IPM into the deployment landscape for wheat, potatoes and grain legumes"), grant agreement 101135348
Related resources
  1. Vexler L, Clot CR, Byrne S et al. k-mer analysis of publicly available resources enables rapid development of an improved KASP marker linked to the H1 resistance locus in potato [version 1; peer review: awaiting peer review]. Open Res Europe 2026, 6:342 (https://doi.org/10.12688/openreseurope.23753.1)
  2. Meade, F., Byrne, S., Griffin, D. et al. Rapid Development of KASP Markers for Disease Resistance Genes Using Pooled Whole-Genome Resequencing. Potato Res. 63, 57–73 (2020). https://doi.org/10.1007/s11540-019-09428-x
  3. Zenodo record 19629845, Version v1, published 17 April 2026, in the IPMorama community: https://doi.org/10.5281/zenodo.19629845
Provenance information Publicly available bulked resequencing data from Meade et al. (2020) were downloaded from the read archives (ESM S1). The new KASP assays were validated on potato breeding material across three years, with PCN resistance phenotypes. k-mers were counted in resistant and susceptible sequencing pools, and H1-associated k-mers extracted by set subtraction (CoSSA), testing several depth thresholds (ESM S2, S3). The retained k-mers were mapped to the DM reference genome to identify candidate SNPs near the 57R region (ESM S5). Two SNPs were converted to KASP assays and their classification accuracy compared with the previously published marker against phenotypic PCN resistance (ESM S4)