**Characterization of the Common** *Japonica***-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (***Oryza sativa* **L.)**

**Jeonghwan Seo 1, So-Myeong Lee 1,2, Jae-Hyuk Han 3, Na-Hyun Shin 3, Yoon Kyung Lee 1, Backki Kim 1, Joong Hyoun Chin 3,\* and Hee-Jong Koh 1,\***


Received: 23 April 2020; Accepted: 14 May 2020; Published: 18 May 2020

**Abstract:** The inter-subspecific crossing between *indica* and *japonica* subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of *japonica*-originated alleles. Interestingly, the HYVs shared *japonica*-originated genomic regions on nine chromosomes, although they were developed through di fferent breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the *japonica*-originated genomic regions and 16 additional trait-specific SNPs. As expected, the *japonica*-originated genomic regions were only present in the *japonica* (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The *Wx* gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as *indica* alleles in HYVs. The *japonica*-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.

**Keywords:** rice; yield; HYV; Tongil; *indica*; *japonica*; SNP; molecular breeding
