Microsatellite/SSR dataset: pomological and molecular characterization of apple cultivars (Malus × domestica Borkh.) of the German Fruit Genebank, Version 1

The German Fruit Genebank (https://www.deutsche-genbank-obst.de/) is a decentralized network with focus on the coordination of the different germplasm collections in Germany to conserve and utilize genetic resources of native fruit species. Here, emphasis is put on the trueness-to-type of the genetic resources based on pomological and molecular characteristics. Over the years from 2009 to 2025, several projects were carried out to take an inventory of the germplasm collections in the apple (Malus ×domestica) network of the German Fruit Genebank. In a first step, at least two knowledgeable experts of the German Pomological Association characterized accessions pomologically. In a second step, a DNA fingerprint analysis was used for the molecular characterization. The DNA fingerprint analysis utilized a set of 17 simple sequence repeat (SSR) markers and 8 reference genotypes recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR; http://www.ecpgr.cgiar.org/) Malus/Pyrus working group and was performed by Microsynth ecogenics GmbH (Balgach, Switzerland). 9,162 samples (fruits/ leaves) of apple trees belonging to the German Fruit Genebank from eight network collections were investigated. 1,565 different (synthetic) genetic fingerprints in correspondence to cultivars could be estimated for apple. The updated version integrates the additional molecular characterization data of project 2824BE001.