Dneasy plant kit

Following centrifugation, cell pellets were re-suspended in Tissue and Cell Lysis Buffer (DNeasy Plant kit; Qiagen, Hamburg, Germany) and transferred into a 2 ml cryovial containing acid-washed glass beads (Sigma-Aldrich, Steinheim, Germany). Cell lysis was achieved with a Bio101 FastPrep instrument (Thermo, Savant Illkirch, France) run at maximum speed (6.5 ms⁻¹) for 45 s. DNA extraction proceeded according to the DNeasy Plant kit protocol.

The DNA used for SNP-genotyping in this survey was extracted from young leaves collected from a tree of each genotype at the beginning of the vegetative phase with the Qiagen DNeasy Plant Kit and further quantified with a Nanodrop ND-8000 (ThermoScientific, USA). The SNP marker data were obtained with the HiScan (Illumina, USA) and the apple 20K SNP chip Infinium array (Illumina, USA); the chip was assembled within the framework of the European project FruitBreedomics^{42 (link)}. The genotyping output was initially analyzed with the software GenomeStudio and further re-edited with ASSiST^{43 (link)}. SNPs with minor allele frequencies lower than 0.05 and call rate below 0.2 were filtered out with the package ‘snpStats’⁴⁴ . The final set of markers successfully recovered in the population consisted of 8,294 biallelic SNPs.