Whole-Genome Sequencing Revealed a Late-Maturing Isogenic Rice Koshihikari Integrated with Hd16 Gene Derived from an Ise Shrine Mutant

We identified the key genes controlling the late maturation of the Japonica cultivar Isehikari, which was found at Ise Jingu Shrine and matures 6 days later than Koshihikari. We conducted a genetics-based approach through this study. First, the latest mature plants, which flowered later than Isehikari, were segregated in the F(2) and F(3) generations of Koshihikari×Isehikari. Next, the linkage relationship of a single late-maturing gene with the SSR markers on the long arm of chromosome 3 was inferred by using late-maturing homozygous F(2) segregants. Moreover, genetic analyses of late maturity were conducted through the process of six times of continuous backcross with Koshihikari as a recurrent parent by using the late-maturing homozygous F(3) line as a nonrecurrent parent, thus developing a late-maturing isogenic Koshihikari (BC(6)F(2)). As a result, we elucidated a single late-maturing gene with incomplete dominance that caused the 14-day maturation delay of Koshihikari. The whole-genome sequencing was conducted on both of Koshihikari and the late-maturing isogenic Koshihikari. Then, the SNP call was conducted as the reference genome of Koshihikari. Finally, a single SNP was identified in the key gene Hd16 of the late-maturing isogenic Koshihikari.