This dataset contains SNP data obtained by using the Axiom®Apple480K array (Bianco et al., 2016) on 1355 apple accessions from nine mostly European institutions and 92 apple progeny individuals from two parental combinations. Among the accessions, 1341 are diploid, 12 are triploid, and two are doubled haploid. These data were mainly obtained in the frame of the EU seventh Framework Programme project FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com/). Two dataset versions are available (see tab "Versions"). In Dataset 1.0, the files with root "FruitBreedomics_apple_253K_SNP" are those used for studying apple pedigrees as described in Muranty et al (2020). In Dataset 2.1, the files with root "FruitBreedomics_apple_320K_SNP" are those used for generating high density SNP data for the apple reference population, as described in Jung et al (2020 ; see Métadonnées/Metadata for this publication). The files with the suffix ".bed" are genotyping matrix in plink binary format, the files with the suffix ".bim" contain positions of loci in plink binary format and the files with the suffix ".fam" contain identifiers of the genotypes plink binary format. This format is described at http://zzz.bwh.harvard.edu/plink/data.shtml#bed.