The seed parent of the sake-brewing rice（sake rice） Yamadanishiki is Yamadabo, and the pollen parent is Tankan Wataribune. Hakutsurunishiki was developed by Hakutsuru Sake Brewing Co., Ltd. to obtain a high-quality sake rice cultivar comparable to Yamadanishiki. The seed parent of Hakutsurunishiki is Yamadabo（Kyushu Univ：KU1713）, and the pollen parent is Wataribune 2（N10484）. Previous research has revealed that Yamadanishiki and Hakutsurunishiki share many similarities in phenotypes and genetic characteristics but also have differences. For the further analysis of the genetic background of Yamadanishiki and Hakutsurunishiki, we attempted to elucidate the genetic background by comparing the whole-genome information of related lines of Yamadanishiki. As a results of phylogenetic tree analysis, it was found that the three lines of Yamadabo（Shin yamadabo 1, Yamadabo（Kyoto University）, Yamadabo（Kyushu University））, the seed parent of Yamadanishiki, and the three lines of Wataribune（Wataribune（Kyushu University）, Wataribune 2, Shigawataribune 2）, the pollen parent of Yamadanishiki, are very closely related. Furthermore, DNA polymorphisms of the Yamadabo and Wataribune lines were compiled from DNA polymorphism analysis and phylogenetic tree analysis. Further analysis revealed that Yamadanishiki is closely related to Yamadabo, and Hakutsurunishiki is closely related to Wataribune. In addition, a detailed whole-genome comparative analysis suggested that the short culm phenotype was inherited by Hakutsurunishiki, inheriting the short arm locus on chromosome 1 from Wataribune 2.