KAI54S
We constructed a Multiplexed ISSR Genotyping by sequencing PCR (MIG-seq) library with two polymerase chain reactions (PCR)(Matsuki et al. 2015). The PCR products were selected and cleaned by library size using AMPure XP (Beckman Coulter, Brea, CA, USA). The sequencing of the multiplexed library was performed using MiSeq Reagent Kit v3 (150 cycle) (Illumina, San Diego, CA, USA) with an Illumina MiSeq Sequencer. Both ends of the fragments and index sequences were read by paired-end sequencing (reads 1 and 2). The reads including adapter and low-quality sequences were filtered and the first and last nucleotides were trimmed using Trimmomatic. As Matsuki et al. 2015, read 1 and read 2 were combined into one file to be treated as independent reads.