Rad-Seq of Theobroma cacao: S_2a
each extracted DNA was normalized to 500 ng and subjected to double enzymatic digestion at 37 C ON with 2 units of each of the enzymes BsaXI and CspCI (New England BioLabsInc). After digestion, a size selection of fragments with 0.9X and 0.12X of Agencourt AMPure XP Beads magnetic beads (Beckman Coulter, Brea, CA, USA) was performed. The DNA was then prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabsInc) with the following modifications: after adapter ligation, a clean with 0.4X and 0.2X of AMPure XP Beads was performed. The number of fragments was increased by PCR with 14 cycles and then, a final cleaning with AMPure XP Beads was performed at a concentration of 0.9X.