GBS data of Malus domestica: young leaf
Genotyping-by-sequencing (GBS) libraries were prepared following a modified ApeKI-based protocol. Briefly, 250 ng of genomic DNA per sample was digested with ApeKI (New England BioLabs, USA) at 75 C for 3 h, followed by ligation of barcoded adapters (4?9 bp unique barcodes per sample) using T4 DNA ligase. Up to 96 barcoded samples were pooled per library, purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel), and amplified by multiplex PCR with Illumina index primers. PCR products were size-selected (400?700 bp) using SPRIselect beads, and library quality was assessed with an Agilent 4200 TapeStation. Sequencing was performed on an Illumina NovaSeq 6000 platform to generate 151 bp paired-end reads.