Abstract: 【Objective】To accurately assess genetic effect of alleles from japonica in a genetic background of indica and to efficiently utilize inter-subspecific heterosis between indica and japonica. 【Method】We have developed a set of novel population with 88 candidate introgression lines (ILs) through backcross program and marker-aided selection, which using japonica variety Nipponbare as donor and indica variety Zhenshan97B as recurrent parent. Each of the ILs contains single one or few japonica introgression segments within the uniform indica genetic background, and together all the introgression segments can cover the whole japonica genome. The genetic effects of each introgression segment in the 88 ILs were analyzed on yield and its component traits including number of tillers, grains per panicle and 1000-grain weight. 【Results】Twenty nine quantitative trait loci (QTLs) with significant effects were detected, of those 6 QTLs had positive additive and overdominant effects, 23 QTLs had negative additive and overdominant effects. 【Conclusion】 Some favorable alleles from japonica could increase yield or its components in the indica background. The overdominant effects play important role in heterosis of intersubspecies.