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

TL;DR

Researchers used advanced sequencing to map a potato resistance gene locus, improving understanding of disease resistance in potatoes.

Contribution

A phased genome assembly and association genetics were used to reconstruct the H1 resistance locus in potato.

Findings

The H1 resistance locus was mapped to chromosome 5 with recombination points identified.

A dihaploid potato line enabled reduced genomic complexity for detailed locus analysis.

Oxford Nanopore sequencing provided a phased haplotype of the H1 interval.

Abstract

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.

The online version contains supplementary material available at 10.1007/s00122-026-05179-9.

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