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

The inter-subspecific crossing between and 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 -originated alleles. Interestingly, the HYVs shared -originated genomic regions on nine chromosomes, although they were developed through different 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 -originated genomic regions and 16 additional trait-specific SNPs. As expected, the -originated genomic regions were only present in the (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as alleles in HYVs. The -originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.