Artificial hybrid breeding can optimize parental traits to cultivate excellent hybrids with enhanced economic value. In this study, we investigated the growth performance and transcriptomes of Gymnocypris przewalskii (♀) and Gymnocypris eckloni (♂) and their F1 hybrid fishes. Hatched individuals of G. przewalskii (GP) and G. eckloni (GE) of the same size and their F1 hybrids (GH) were separately cultured for eight months in three cement tanks (n = 3). The growth indexes were measured, which showed that the growth rate of the groups was GE > GH > GP, while the survival rate was GH > GE > GP. The RNA-Seq data analysis of the muscles from the three Gymnocypris fish strains revealed that gene transcription has a significant impact on F1 hybrid fish and its parents. The differentially expressed genes (DEGs) in GH show less differences with GP, but more with GE. qRT-PCR was used to confirm the expression profiles of the chosen DEGs, and the results showed positive correlations with the RNA-seq data. KEGG enrichment results indicated that the DEGs were related to a variety of molecular functions, such as glycolysis/gluconeogenesis, arachidonic acid formation, citrate cycle, and the MAPK, PI3K-Akt, or mTOR signal pathways. Subsequent analysis indicated that there may be a significant correlation between the differential expression of IGF2 and a difference in the growth of GE and GP.

Hybrid breeding is an effective approach to generate better varieties and prevent variety degradation. The present study investigated the metabolic changes underlying growth superiority in the novel Gymnocypris hybrid (GH), Gymnocypris przewalskii ♀ (GP) × G. eckloni ♂ (GE). The ranking of survival rate was GH > GE > GP, whereas the ranking of growth rate was GE > GH > GP. A proteomic analysis of G. hybrid and its parents was conducted to elucidate the metabolic changes underlying growth superiority. Identified pathways were primarily associated with amino acid, carbohydrate, energy, lipid, and nucleotide metabolism. These metabolic pathways, which are closely associated with growth, are controlled through regulation of the expression of numerous proteins, including adenosylhomocysteinase, hydroxypyruvate reductase, glutamate-cysteine ligase, L-lactate dehydrogenase, creatine kinase, GDP-L-fucose synthase, pyruvate kinase, fructose-bisphosphate aldolase, carbonic anhydrase, phosphopyruvate hydratase, phosphoglycerate kinase, S-(hydroxymethyl) glutathione dehydrogenase, and AMP deaminase. Real-time PCR assays showed that the level of mRNA expression of differentially expressed genes was positively correlated with growth. Proteins that were differentially expressed in GH exhibited fewer differences from GP and more differences from GE. These data are the first to reveal the molecular mechanism whereby growth is regulated in G. hybrid and its parents at the protein level. The study thus provides important information for genetic breeding and improvement of G. hybrid for aquaculture production.