**1. Introduction**

There are two subspecies in cultivated rice (*Oryza sativa*), *indica* and *japonica*. *Indica* rice is known to be adaptable to tropical regions, while *japonica* rice is grown in temperate regions. Therefore, *indica* and *japonica* have di fferent characteristics [1]. In general, *japonica* varieties are known to have relatively low yield potentials, as compared to *indica* varieties. To improve the yield potential of *japonica* rice, inter-subspecific crosses between *indica* and *japonica* have been conducted by conventional rice breeders [2]. As a result of these e fforts, several high-yielding varieties (HYVs) have been developed from *indica*-*japonica* crosses. One of the greatest historical successes of *indica*–*japonica* crosses was the development of Tongil, an HYV, in Korea. Tongil showed a 30% higher yield than those of the conventional *japonica* varieties. By growing Tongil rice, self-su fficiency in staple food in Korea was possible in 1977 [3]. There were important trade-o ffs in growing Tongil, such as cold intolerance, pathogen susceptibility, and low eating quality, which were inherited from *indica* parents. A series

of 'Tongil-type' HYVs have been developed from *indica*–*japonica* crosses to overcome the vulnerable points of Tongil from the late 1970s [2].

HYVs have been developed in Japan using *indica* and *japonica* varieties since the 1980s. Takanari is a Japanese semi-dwarf HYV, developed from the crosses between Milyang 42 and Milyang 25. Takanari shared the ancestry of Tongil [4]. To date, it recorded the highest grain yields for both yield trials (>10 t/ha as brown rice) and individual trials (11.7 t/ha as brown rice) in Japan [5]. Minghui 63, which was derived from the cross between IR 30 and Gui 630, is the male parent of the elite hybrid rice Shanyu 63 from China. IR 30 is a semi-dwarf variety developed in IRRI (International Rice Research Institute) and is a restorer line for WA-CMS A-lines, which have a good plant type, a high resistance to blast, a bacterial blight, and brown planthoppers. Gui 630 is a rice germplasm from Guyana that has a high grain weight, desirable grain quality, and high yield potential [6]. Gui 630 is known as an *indica* restorer variety [7]. Minghui 63 was classified into the *indica II* subpopulation, together with Milyang 23 and some other *indica-japonica* HYVs, by genome sequence analysis [8].

Nipponbare is the *japonica* reference genome of rice and was first sequenced at the high-quality whole-genome level through all the crops [9]. In addition, the whole genome sequences of *indica* rice varieties were reported [10–14]. The genomic difference between *indica* and *japonica* at the sequence level has been extensively studied [15]. At least 384,431 single nucleotide polymorphisms (SNPs) and 24,557 insertion/deletion mutations (InDels) were reported between Nipponbare and 93-11 [16]. With the advent of Next-Generation Sequencing (NGS) technology, numerous genomes of diverse rice germplasm collections have become available. For instance, 3000 rice genomes were sequenced and deployed in genetic and genomic rice studies [17–20]. Recently, more than one hundred high-yielding loci, associated with green revolution phenotypes and derived from the two ancestral *indica* varieties, were identified with the help of pedigree analysis, whole-genome sequencing, and genome editing [21]. Furthermore, most of the quantitative trait loci (QTLs) and genes for high-yielding potential in HYVs originated from *indica* parents in previous studies using HYVs derived from *indica*–*japonica* crosses [3–5,22,23]. No report exists on the characterization of *japonica* genomic regions in HYVs derived from *indica*–*japonica* crosses yet.

Previously, we sequenced the whole genomes of Tongil and its parental varieties to analyze the genome composition and genetic factors of Tongil. As a result, the Tongil genome was found to be derived mostly from the *indica* genome, with a small portion of *japonica* genome introgressions [3]. This study was carried out to comparatively analyze the genome structure of eight HYVs and to identify the *japonica*-originated genomic regions that are shared in HYVs, which will be helpful in understanding the role of *japonica* genome in Tongil and other HYVs that are developed in temperate regions for the further development of promising HYVs.
