Although many semidwarf genes allelic to sd1 have been identified in different cultivars (DGWG, Jukkoku, Reimei, and Calrose 76), differences in their influences have not been elucidated. Thus, investigating the differences in ecological and phenotypic traits in relation to yield between d60- and sd1-carrying plants, as well as those among sd1 allelic variants of different origins, will be beneficial for future use of d60 and multiple allelic variants of sd1. The first author developed isogenic semidwarf lines by continuously backcrossing sd1 of Jukkoku (Jukkoku_sd1) and sd1 of Kinuhikari (IR8_sd1) and d60 and both genes into the Koshihikari background and maintained the lines to investigate the resulting traits. Hence, the study was conducted with the following specific objectives: (a) investigate and quantify the differences between d60- and sd1-carrying NILs, in relation to yield, to assess the utility of sd1 and d60 semidwarf genes and (b) sequence NILs by MiSeq to detect the differences between Sd1/sd1 target sites.