Phased potato genome assembly and association genetics enable delineation of the H1 resistance locus against potato cyst nematodes

Yuk Woon Cheung, Lynn H. Brown, Thomas M. Adams, Brian Harrower, Amanpreet Kaur, Gaynor McKenzie, Jamie Orr, James Price, Vikrant Singh, Moray Smith, Micha Bayer & Ingo Hein

Theoretical and Applied Genetics; March 12 2026; vol. 139; article 92

The complexity of potato genetics, characterised by tetrasomic inheritance, has contributed to slower genetic gain in potato compared to other major crops. Disease resistance genes, often found in large clusters of highly similar paralogs and alleles, further complicate genetic studies. The H1 resistance locus, introgressed into potato cultivars from Solanum tuberosum ssp. andigena, has been successfully used for over 60 years to control Globodera rostochiensis in Europe. Although previous genetic studies mapped this resistance to chromosome 5, the complete structure of the locus remained elusive. To reduce genomic complexity, we generated a dihaploid of the cultivar ‘Athlete’, DH4_Athlete, carrying the H1 resistance locus, and produced a phased haplotype representation of the H1 interval using Oxford Nanopore sequencing. Combined with RenSeq-based association genetics, this approach allowed us to reconstruct the entire H1 locus, including recombination points at both the 5′ and 3′ ends of the interval.

See https://link.springer.com/article/10.1007/s00122-026-05179-9

Figure 1: SMRT-AgRenSeq-d analysis of H1. A Identification of NLR containing contigs in the reference cultivar ‘Buster’ with association to H1. Columns on the x-axis represent NLR containing contigs, with dots indicating mapped k-mers and their AgRenSeq-derived association score to H1 resistance. The dashed line highlights the chosen threshold (50% of the maximum = 29) for inclusive candidate selection. B F1 scores and number of candidate NLRs for each association score group. C The predicted positions of H1 candidates with F1 score > 0.95 are shown (red dots) in relation to all NLRs from reference Buster mapped onto DM v6.1 over all 12 chromosomes