Tracing modern breeding introgressions in European potato

The European potato germplasm originated from a few founding genotypes, and its narrow genetic base has since been broadened through introgressions from wild relatives. We combined pedigree records and genome-wide SNP data to trace the origin, spread, and contributing ancestors of modern breeding introgressions in Europe. We first used a curated pedigree database to identify the Major Contributing Ancestors (MCAs) of 1209 varieties from the European Common Catalogue, revealing influential cultivars such as Katahdin, Saskia, and Agria as the top contributors to the modern European gene pool. Building on this framework, we developed a modified MCA approach that uses SNP alleles to trace the spread of haplotypes that were introduced into the European germplasm after 1945; two of which now occur in half of European varieties. Using the pedigree database to find the origin of these modern introgressions, we traced key contributions from S. vernei, S. demissum, and S. tuberosum Group Andigena clone CPC 1673. We observed multiple distinct haplotypes of the R3a/b late blight resistance introgression on chromosome 11. Additionally, we generated a genome assembly of S. demissum to validate a single sub-genome origin of the R3a/b introgression. We also traced a putatively starch-associated introgression derived from S. vernei. Our framework links historical breeding records with genomic data, revealing the legacy of modern introgression breeding in the European germplasm.