Transcriptomic profiling of skeletal muscle unravels the molecular networks underlying growth divergence in the Japanese eel ( <i>Anguilla japonica</i> )

The Japanese eel ( Anguilla japonica ) is an important aquaculture species in East Asia, but pronounced growth heterogeneity within cultured populations remains a major constraint to production efficiency. To investigate the molecular basis of growth retardation, this study compared the dorsal muscle transcriptomes of fast-growing eels (FGEs) and slow-growing eels (SGEs) after an 8-week feeding trial. RNA-seq was performed on individuals with extreme growth phenotypes. A total of 638 differentially expressed genes (DEGs) were identified, including 186 upregulated and 452 downregulated genes in FGE relative to SGE. Functional enrichment analysis showed that FGE preferentially upregulated genes involved in lipid transport, amino acid and carbohydrate metabolism, and muscle structural assembly, indicating a favorable anabolic state. In contrast, SGE exhibited significant enrichment of pathways related to p53 signaling, circadian rhythm, PPAR signaling, and cardiomyopathy-associated structural remodeling. Several stress- and growth-inhibitory genes, including igfbp3 , mstn , socs3 , gadd45α , and sesn1 , were highly expressed in SGE. In contrast, genes associated with nutrient utilization and myofiber development, such as fabp7 , apoe , and actc1 , were more highly expressed in FGE. qRT-PCR validation confirmed the reliability of the transcriptomic results. These findings suggest that growth retardation in A. japonica is associated with stress-induced anabolic inhibition, metabolic reprogramming, circadian disturbance, and impaired muscle structural development, rather than simply reduced nutrient supply. This study provides new insight into the molecular mechanisms underlying growth heterogeneity in A. japonica aquaculture.