SNP genotyping Dutch heritage apple cultivars allows for germplasm characterization, curation, and pedigree reconstruction using genotypic data from multiple collection sites across the world

Abstract

AbstractThe curation and preservation of Dutch apple germplasm depends on reliable accession level information. However, many accessions of Dutch heirloom apple cultivars maintained publicly by the “Centre for Genetic Resources, the Netherlands” (CGN) and privately by Dutch pomological societies lack information regarding true-to-typeness and pedigree ancestry. The aim of this study was to address this knowledge gap by genotyping 652 apple accessions maintained in the CGN collection and Dutch private collections, compare their genotypic information to each other and to a large database of apple cultivars from around the world to identify genotypic duplicates and pedigree relationships for the Dutch apple cultivars. Towards this aim, accessions were genotyped on the 20 K Illumina Infinium(R) apple SNP array and with 15 SSR markers. Each accession was assigned to a genotypic profile code (MUNQ codes, as used in previous studies) facilitating communication regarding genotypic duplicates. There were 211 (51.1%) genotypic profiles in the Dutch germplasm which were not identified in other germplasm collections. Private collections maintained many of these unique accessions, including important pedigree ancestors. The study identified a number of common pedigree ancestors of Dutch cultivars, such as ‘Herfst Bloem Soete’, ‘Huismanszoet’ (2), and ‘Reinette Rouge Étoilée’. The duplicate and pedigree reconstruction results and relevant literature descriptions were used to pomologically verify the identity of relevant accessions. The results of this study resolved identity disputes, helped to decide which accessions should be retained or included in the CGN collection, and benefited ongoing pomological studies in ancestry and provenance of traditional Dutch cultivars.