| Summary: | We developed semidwarf and late-maturing isogenics of Koshihikari to stabilize high yield and avoid high temperature maturation. Whole-genome analysis (WGS) was conducted to examine the transitional changes in the entire genome, the size of DNA fragments integrated with the target gene, and genes accompanying the target gene owing to the progress of backcrossing. In both Koshihikari Hd16 (BC<sub>7</sub>F<sub>4</sub>) and Koshihikari sd1Hd16 (BC<sub>8</sub>F<sub>2</sub>), an SNP from adenine to guanine was detected in <i>Hd16</i> at 32,996,608 bp on chromosome 3, which is known to be a causative mutation of <i>Hd16</i> in Nipponbare. In Koshihikari sd1Hd16 (BC<sub>8</sub>F<sub>2</sub>), an SNP from thymine to guanine was detected in <i>sd1</i> at 38,267,510 bp on chromosome 1. From BC<sub>7</sub> to BC<sub>8</sub>, the size of the DNA fragment integrated with <i>Hd16</i> decreased by 5871 bp. Koshihikari sd1Hd16 flowered 12.1 days later than Koshishikari or Koshihikari sd1 did and was 14.2 cm (15%) shorter than Koshihikari. The yield in Koshishikari sd1Hd16 (63.2 kg/a) was 7.0% higher than that of Koshihikari. This is a new germplasm designed to avoid heat damage at ripening during high-temperature summer periods by late maturation owing to <i>Hd16</i> as well as to avoid lodging by autumn typhoons by semidwarfness owing to <i>sd1</i>.
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