**5. Conclusions**

Baegilmi is a *japonica* rice cultivar with extremely early heading that is useful for diversifying cropping patterns in Korea. From the Koshihikari × Baegilmi RIL population, we detected three QTLs for days to heading, *qDH3*, *qDH6*, and *qDH7*. Di fferent allelic combinations of the three QTLs in the RIL population provided breeding lines that can be useful for developing high quality *japonica* rice cultivars inheriting Koshihikari's high eating quality with varying DH. Screening Korean rice cultivars for the allelic compositions of *Hd16* (A/G SNP), *Hd1* (43 bp Indel), and *Ghd7* (1.9 kb Indel) underlying *qDH3*, *qDH6*, and *qDH7*, respectively, showed that few cultivars carry one or more alleles for early heading at the three genes, suggesting that DH can be further accelerated and fine-tuned in breeding programs by using the allelic variations in *Hd16*, *Hd1*, and *Ghd7*.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/11/9/957/s1, Supplementary Figure S1: Linkage map from the Koshihikari × Baegilmi RIL population (*n* = 142) using 128 SNP markers, Supplementary Table S1: Molecular markers designed to genotype sequence polymorphisms in *Hd16*, *Hd1*, and *Ghd7*, Supplementary Table S2: Allelic distributions of the polymorphisms in *Hd16*, *Hd1*, and *Ghd7* in 295 Korean commercial rice cultivars.

**Author Contributions:** Conceptualization by Y.M. and J.-U.J.; phenotype evaluation and data curation by J.-M.J., S.-K.H., J.K., and C.L.; genotyping analysis by G.P.L.; statistical analysis by Y.M. and J.-U.J.; writing—original draft preparation by Y.M.; writing—review and editing by J.-U.J.; project administration by Y.M. and J.-U.J. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by Rural Development Administration (RDA), Republic of Korea, gran<sup>t</sup> number PJ01357205.

**Acknowledgments:** We thank Sunghee Kim and Kyoungran Yoo for providing excellent technical supports.

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