The crosstalk between naive nucleus and maternal factors deposited in egg cytoplasm before zygotic genome activation is crucial for early development of vertebrates. However, it is difficult to clarify the relative roles of zygotic and cytoplasmic factors in normal developing embryos, in which both types of factors were derived from the same species. Cross-species nuclear transfer provides an ideal system to study the relative role and crosstalk between egg cytoplasm and zygotic nucleus in development. In most studies of nuclear transplantation, the cloned animals were obtained by intraspecies nuclear transfer and are phenotypically identical to their nuclear donors. In fishes, however, cross-species nuclear transplantation could be achieved in quite a few species. By transferring nuclei from transgenic common carp (Cyprinus carpio) into enucleated eggs of goldfish (Carassius auratus), we generated seven cross-genus cloned transgenic fish. Nuclear genomes of the cloned fish were exclusively derived from the nuclear donor species, common carp, whereas the mitochondrial DNA from the donor carp gradually disappeared during the development of nuclear transfer (NT) embryos. The somite development process and somite number of nuclear transplants were consistent with the recipient species, goldfish, rather than the nuclear donor species, common carp. This resulted in a long-lasting effect on the vertebral numbers of the cloned fish, which belonged to the range of goldfish. These demonstrate that fish egg cytoplasm not only can support the development driven by transplanted nuclei from a distantly related species at the genus scale but also can modulate development of the nuclear transplants. Although cross-species NT could be used to retain the genetic viability of a species near extinction, most embryos produced by cross-species NT were unable to develop to later stages due to incompatible nucleo-cytoplasmic interactions between the donor nuclei and the recipient cytoplasm from different species. To study the early nucleo-cytoplasmic interaction in cross-species NT, two laboratory fish species, zebrafish (Danio rerio) and Chinese rare minnow (Gobiocypris rarus), from different subfamilies were used to generate cross-subfamily NT embryos. Suppression subtractive hybridization (SSH) was performed to screen out differentially expressed genes from the forward and reverse subtractive cDNA libraries. After dot blot and real-time PCR analysis, 80 of 500 randomly selective sequences were proven to be differentially expressed in the cloned embryos. Among them, 45 sequences shared high homology with 28 zebrafish known genes, and 35 sequences were corresponding to 22 novel expressed sequence tags (ESTs). Based on functional clustering and literature mining analysis, the up- and down-regulated genes in the cross-subfamily cloned embryos were mostly found to be relevant to transcription and translation initiation, cell cycle regulation, protein binding, etc. Therefore, it is concluded that the fish egg cytoplasm could not only support the division and development of nuclei from another species, but also exert impact on the cellular homeostasis of the cross-species clones at different levels of biological processes. Zebrafish and Chinese rare minnow were also utilized to produce mutual crossbred embryos, zebrafish ♀ X Chinese rare minnow ♂ (ZR) and Chinese rare minnow ♀ X zebrafish ♂ (RZ), and to examine the impact of cytoplasm from different species on a common type of nucleus. Although these two types of crossbred embryos originated from common nuclei of the same genetic materials, various developmental capacities were gained due to different origins of the egg cytoplasm. Using cDNA amplified fragment length polymorphism (cDNA-AFLP), we compared transcript profiles between the mutual crossbred embryos at two developmental stages (50%- and 90%-epiboly). Three thousand cDNA fragments were generated in four cDNA pools with 64 primer combinations. All differentially displayed transcript-derived fragments (TDFs) were screened by dot blot hybridization, and the selected sequences were further analyzed by semi-quantitative RT-PCR and quantitative real-time RT-PCR. Compared with ZR embryos, 12 genes were up-regulated and 12 were down-regulated in RZ embryos. The gene fragments were subjected to BLASTN analysis. The sequences encoded various proteins which functioned at various levels of proliferation, growth, and development. One gene (ZR6), dramatically down-regulated in RZ embryos, was chosen for loss-of-function study. The knockdown of ZR6 gave rise to the phenotype resembling that of RZ embryos. All these evidences reveal that fish nucleus developing in the circumstance of egg cytoplasm could be largely influenced by the cytoplasmic factors. Therefore, developmental process should be interpreted in a systematic way rather than in a way that solely focuses on the role of nuclear genome.