title: Capture sequencing of a Malus domestica panel of diversity
design: Probes targeting the apple genes were commercially synthetized by MYcroarray in a custom MYbaits kit (Daicel Arbor Biosciences, MI, USA). Total genomic DNA was extracted from dried leaves using an automated method, adapted from Risterucci et al. (2009), on a Biomek FXP (Beckman Coulter, CA, USA) and the NucleoMag Plant Kit (MachereyNagel, Dren, Germany). DNA was quantified and normalized to a 15 ng/L concentration with a Fluoroskan Ascent FL fluorometer (Thermo Fisher Scientific, MA, USA). NGS sample library construction was performed with 1 g of DNA per accession, using a preparation protocol developed at the GPTRG Facility at CIRAD (UMR-AGAP Institute, Montpellier, France) and adapted from Meyer et al. (2010) and Kircher et al. (2012). DNA samples were sheared to an average length of 300 bp on a Bioruptor Standard instrument (Diagenode, Lige, Belgium; Cat No. UCD-200). Sequence capture by hybridization was performed according to the manufacturers protocol (v.2) for the MYbaits target capture kit with the custom oligonucleotide library designed by Daicel Arbor Biosciences. Sequencing-by-synthesis was performed on a HiSeq2500 with a HiSeq Rapid SBS Kit v2 from Illumina (San Diego, U.S.A.) in 2 x 250 bp paired-end read mode at the Max Planck-Genome-centre Cologne (MP-GC) (Cologne, Germany).