This dataset corresponds to the genotypic data used for the elite material in the FBo-Hi panel used by Cazenave et al (2021) "Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple" G3: Genes, Genomes, Genetics. The dataset was obtained using the 20K apple SNP array (Bianco et al, 2014). These data were 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/).