| Summary: | 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 <i>Gymnocypris przewalskii</i> (♀) and <i>Gymnocypris eckloni</i> (♂) and their F1 hybrid fishes. Hatched individuals of <i>G. przewalskii</i> (GP) and <i>G. eckloni</i> (GE) of the same size and their F1 hybrids (GH) were separately cultured for eight months in three cement tanks (<i>n</i> = 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 <i>Gymnocypris</i> 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.
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