**5. Conclusions**

Consumer preference in grain shape and quality during conventional breeding procedures, without sacrificing the high-yield potential of *indica*, were revisited by the genomic analysis of HYVs. The 14 *japonica*-originated genomic regions and alleles identified in this study shared by HYVs could be applied in further development of more HYVs through inter-subspecific rice breeding in temperate rice.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/11/5/562/s1, Figure S1: Pedigrees of eight HYVs used in this study. (A) Tongil, (B) Minghui 63, (C) Cheongcheongbyeo, (D) Milyang 23, (E) Nampungbyeo, (F) Hanareumbyeo, (G) Dasanbyeo, (H) Takanari. Table S1: The list of 94 diverse rice germplasms used in this study. The order of ger1mplasm is identical with order in Figure 3. The varieties highlighted by yellow are eight HYVs used in this study. Table S2: The list of 54 Fluidigm SNP markers used in this study. MAF, Heterozygosity and PIC were calculated in 94 rice varieties.

**Author Contributions:** Conceptualization, J.H.C. and H.-J.K.; methodology, J.S. and J.H.C.; software, J.S.; validation, B.K. and J.H.C.; formal analysis, J.S. and S.-M.L.; investigation, J.S., S.-M.L., J.-H.H., N.-H.S., and Y.K.L., resources, J.H.C and H.-J.K.; data curation, J.S. and B.K.; writing—original draft preparation, J.S.; writing—review and editing, J.H.C. and H.-J.K.; visualization, J.S., S.-M.L., and J.H.C.; supervision, H.-J.K.; project administration, J.H.C.; funding acquisition, H.-J.K. All authors have read and agreed to the published version of the manuscript.

**Funding:** This study was funded by a gran<sup>t</sup> from the Next-Generation BioGreen 21 Program (No. PJ013165) of the Rural Development Administration, Korea.

**Acknowledgments:** We appreciate to members of Crop Molecular Breeding Lab., in Seoul National University for their kind advice and assistance for this study.

**Conflicts of Interest:** The authors declare no conflict of interest.
