The definition of dominance or epistasis is generally on the basis of a descriptive characterization for these crops in the field, such as yield per hectare and the weight of grain. Since these trait examinations lack molecular information, how to precisely predict the phenotypic changes in filial generation is still a problem in heterosis studies. For rice, the genetic information caused by hybridization can be archived through analyzing of proteomes of rice seeds. Differential analysis of proteomes was introduced for the rice seeds of three cultivars, 9311, PA64S and LYP9, an elite rice hybrid from cross between 9311 and PA64S. In the three rice endosperms, the expression profiles of proteins were similar with the stained spots of 47 +/- 1, 46 +/- 0.6 and 44 +/- 0.6, for 9311, PA64S and LYP9, respectively; however, the number of proteins expressed in the rice embryos was significantly increased with the stained spots of 395.3 +/- 12.9, 350 +/- 9.2, and 389.3 +/- 16.4, for 9311, PA64S and LYP9, respectively. Importantly, the image comparisons and protein identifications have revealed in significantly different embryo protein spots among the three rice cultivars. By carefully analyzing these different 2-DE spots, many of them from the three embryos were shown to display a mirrored relationships between parents and the first filial generation. Furthermore, all of stained spots in LYP9 embryo were found on the 2-DEs from its parents, indicating that there was a genetic linkage. These results suggest that proteomic approach is able to serve pedigree analysis and functional prediction for new rice breeds.