*2.2. Whole Genome Sequencing and DNA Variation*

Tongil and its three parental varieties (Yukara, IR 8, and TN1) were sequenced in a previous study [3]. The other eight varieties were sequenced in this study using the Illumina Hiseq 1000 and NextSeq 500 platform (Illumina, San Diego, CA, USA) (Table 1). Whole genome sequencing, including the construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer. The Illumina whole-genome shotgun paired-end DNA sequencing data were filtered to obtain high-quality sequence data. Raw sequence reads were subjected to quality trimming using FastQC v0.11.3 (http://www.bioinformatics.babraham.ac.uk/ projects/fastqc/), and the reads with a Phred quality (Q) score <20 were discarded. Adapter trimming was conducted by using Trimmomatic version 0.36 (http://www.usadellab.org/cms/?page=trimmomatic).

The clean reads were mapped on the *japonica* reference Nipponbare genome (Os-Nipponbare-Reference-IRGSP-1.0 [24]) using the Burrows–Wheeler Aligner (BWA) program version 0.7.15 [25]. The alignment results were merged and converted into binary alignment map (BAM) files [26]. The BAM files were used to calculate the sequencing depth and to identify SNPs using the GATK program version 3.4 with default parameters [27].

All the raw sequence data obtained in this study are available in the NCBI Short Read Archive (SRA) database under the following BioProject accession numbers: Nipponbare [PRJNA264254], Milyang 23 [PRJNA264250], Dasan (or Dasanbyeo) [PRJNA222717], Cheongcheong (or Cheongcheongbyeo) [PRJNA616202], Nampung (or Nampungbyeo) [PRJNA616219], Hanareum (or Hanareumbyeo) [PRJNA616209], Takanari [PRJNA616222], and Minghui 63 [PRJNA616216]. The raw sequence data of Tongil, Yukara, IR 8, and TN1 are available in a previous study [3].
