This dataset corresponds to the curated genotypic data used for the progeny group of the apple reference population used by Jung et al (2020) "The apple REFPOP - a reference population for genomics-assisted breeding in apple" Horticulture Research, 7:189. The dataset was obtained using the 20K apple SNP array (Bianco et al, 2014). These data were obtained partly 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/) and partly in the frame of the INRAE SelGen project GDivSelGen: "Efficient use of genetic diversity in genomic selection".