*2.1. Plant DNA Materials*

The eight HYVs, including Cheongcheongbyeo, Dasanbyeo, Hanareumbyeo, Milyang 23, Minghui 63, Nampungbyeo, Takanari, and Tongil, and four non-HYVs, including Nipponbare, Yukara, IR 8, and TN1 were used for the whole-genome sequence analysis. Cheongcheongbyeo, Dasanbyeo, Hanareumbyeo, Milyang 23, and Nampungbyeo are Tongil-type HYVs that were developed in Korea. Takanari and Minghui 63 are HYVs from Japan and China, respectively. The pedigree of each of the eight HYVs can be found in Figure S1. A total of 94 rice varieties were used for SNP marker validation (Table S1).
