Molecular Mechanisms of Growth Differences in Gymnocypris przewalskii and Gymnocypris eckloni through a Comparative Transcriptome Perspective

Abstract

Genetic composition plays a crucial role in the growth rate of species, and transcriptomics provides a potent tool for studying genetic aspects of growth. We explored the growth rates and transcriptomes of the Cyprinids G. przewalskii (GP) and G. eckloni (GE). A total of 500 individuals of G. przewalskii and G. eckloni, matched in size, were separately cultured for 9 months in six cement tanks (each group with three replicates). Growth indices were measured, revealing that the growth rate of GE was greater than that of GP (p < 0.05), while there was no significant difference in survival rates (p > 0.05). Simultaneously, we conducted RNA-Seq on the muscles of both GP and GE. The results indicated a significant difference of gene expression between GP and GE, identifying 5574 differentially expressed genes (DEGs). Quantitative real-time reverse transcription–polymerase chain reaction of 10 DEGs demonstrated consistency in expression profiles with the results from the RNA-Seq analysis. The DEGs were significantly enriched in glycolysis/gluconeogenesis (ko00010), arachidonic acid formation (ko00061), arginine biosynthesis (ko00220), and the MAPK (ko04013), PI3K-Akt (ko04151), mTOR (ko04150), and TGF-β (ko04350) signal pathways, as revealed by Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. This study also identified some growth-related DEGs, such as IGF2, Noggin, Decorin and others. Notably, the low expression of IGF2 may be a factor contributing to the slower growth of GP than GE.