Whole genomic resequencing analyses of rice plants; japonica cultivars, Notohikari with normal grain, and near-isogenic line of Notohikari with large grain produced by introduction of the gs3 allele of japonica cultivar, Akita 63. Oryza sativa Japonica Group strain:Notohikari

Japonica rice cultivar; Akita 63 had large sink capacity by enlarged grain size, and had the large-grain alleles of gs3. To investigate the effects on the gs3 allele of Akita 63 on the grain size and productivity of rice plants, the near-isogenic line of rice plant was produced by crossing normal-grain japonica cultivar; Notohikari with Akita 63. The NIL with large grain; large-grain Notohikari rice plant possessing the gs3 allele originated from Akita 63. To confirm that the minimal regions including the gs3 allele had been transferred to the genomic gene of Notohikari, next-generation sequencing analysis was performed. Using Os-Nipponbare-Reference-IRGSP-1.0 reference genome, evaluation of genetic diversity of genomic DNA between Notohikari and LG-Notohikari was conducted. The genomic gene regions from approximately 15 to 21 Mb on chromosome 3 of LG-Notohikari has been replaced by the correspondence gene regions including the gs3 allele of Akita 63.