Discovering useful genes, improving agricultural traits hidden in the plant genome, and applying these findings to crop breeding will pave the way for breeding by design. An elite line has a combination of super traits. For example, Shanyou 63 is the best hybrid in China and was produced by crossing Zhenshan 97 with Minghui 63. 131 rice restoring lines germplasm and 249 elite hybrid were obtained from breeding programs for Minghui 63 in China. In molecular breeding, breeders highlight the importance of genetic networks that underlie the complex phenotypes in rice; revealing these networks ultimately lead to a more complete understanding of genetic and molecular bases of quantitative trait variation in rice. For improving the plant high character of rice, the quantitative trait locus of sd-1 gene were used. Although the QTL sd-1 accounts for 59.8% of the total variation, a breeder can control the plant height by utilizing sd-1 and integrating other QTLs that affect plant height. Rice breeding in Japan optimized eating quality and plant height. Highly palatable rice was created by using Koshihikari as the donor parent. Here, we first carried out analysis on high quality QTLs (such as grains low in chalkiness) aggregation; then, some lines were included that had other desirable traits. Ultimately, new varieties were produced, and they integrated many favorable properties.