Rice (Oryza sativa L.) is a major food component of over half of the world’s population, and increased grain yield is a major goal of rice production. Two important yield-related genes are DEP1, regulating inflorescence internode length, and IPA1, involved in plant architecture. The dep1 allele gives rise to a dense, erect panicle shape, while the ipa1 allele leads to a reduced number of tillers and an increased number of grains per panicle. In this study, we focused on the breeding effects of dep1 and ipa1 using two F2 populations derived from cultivars carrying these alleles. Analysis of yield components in the F2 populations revealed that dep1 and ipa1 have contradictory effects, with the exception of number of panicles and spikelet density. The two dep1 and ipa1 alleles can offset each other’s negative advantage for some traits. The performance of yield components is consistent with the requirements of ideal plant type in northeast China once the individuals are heterozygous at two loci. By considering genetic analysis data and previous studies, we speculate that DEP1 and IPA1 loci make genetic contributions of additive, dominance and epistasis effects to yield components. Our results should provide a valuable reference for developing hybrid japonica rice by direct application of F1 plants heterozygous at the two loci and for shortening the breeding period for conventional japonica rice by rapidly fixing superior genotype combinations in early hybrid generations.