Yield is a complex trait. To improve it, the accumulation of the favourable alleles of valuable genes is required for each yield‐related trait. In this study, we used two high‐yielding rice cultivars developed in Japan, indica‐type ‘Takanari’ and japonica‐type ‘Momiroman’, for a genetic analysis of the sink capacity‐related traits. An F2 population showed transgressive segregation for the number of spikelets per panicle. Quantitative trait locus (QTL) analysis detected four QTLs for the trait. Two of the QTLs were most likely identical to previously cloned GN1a and APO1, and their Takanari alleles had positive effects. The Momiroman alleles of the other two QTLs had positive effects, and one of these QTLs was most likely identical to SPIKE/GPS. The QTL on the long arm of chromosome 3 appeared to be novel; it clustered with QTLs for grain length and days‐to‐heading. Substitution mapping revealed that the close linkage of QTLs caused the clustering. These results suggest that the combination of the favourable alleles of detected QTLs could lead to greater sink capacity than that of the parental cultivars.