Comparative Transcriptomic Analysis Reveals Key Growth-Related Genes and Alternative Splicing Events in Siniperca scherzeri

Abstract

Siniperca scherzeri is an important aquaculture species in China with good disease resistance, but its growth rate is relatively slow. To uncover the molecular mechanisms underlying growth trait differences, this study employed RNA-seq technology to analyze the liver tissues of fast-growing (FG) and slow-growing (SG) individuals of S. scherzeri. A total of 875 differentially expressed genes (DEGs) and 622 differentially alternatively spliced genes (DSGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs were mainly involved in skeletal development, extracellular matrix remodeling, signal transduction, and cell growth and apoptosis, whereas the DSGs were significantly enriched in processes such as RNA splicing and processing, protein degradation, ribosome biogenesis, muscle structure and contraction, and were associated with multiple energy metabolism and signaling pathways. Alternative splicing analysis revealed that, compared with the slow-growth group, the fast-growth group exhibited a higher abundance of alternative splicing events. These results suggest that the growth differences in S. scherzeri may stem from the coordinated regulation at both the transcriptional and splicing levels, thereby contributing to enhanced growth rates. These findings provide important insights into the molecular basis underlying growth differences in S. scherzeri and offer valuable resources for the identification of potential molecular markers and key functional genes for aquaculture breeding.