Transcriptome and physiological analysis reveal alterations in muscle metabolisms and immune responses of grass carp (Ctenopharyngodon idellus) cultured at different stocking densities

Grass carp (Ctenopharyngodon idellus) is one of the most common aquaculture fish species around the world. High stocking density applied in the intensive C. idellus culture may have negative impact on fish health and flesh quality. To investigate the effect of stocking density on growth, flesh quality, and immune response of C. idellus, we conducted a comprehensive physiological, biochemical, and transcriptome analysis on fish reared at low stocking density (LSD) (5 fish per tank, 2.45 kg m−3), medium stocking density (MSD) (15 fish per tank, 7.44 kg m−3), and high stocking density (HSD) (30 fish per tank, 14.47 kg m−3), respectively. After 78-day culture, fish maintained at LSD exhibited the highest weight gain, followed by those in MSD and HSD. The highest levels of free amino acid and unsaturated fatty acid components were mostly found in the muscle of either MSD or HSD group. The level of saturated fatty acids (SFAs) with low carbon chains were significantly highest in LSD. However, C17:0-C22:0 SFAs were significantly elevated with the increase in stocking density. Transcriptome profiling of muscle tissue revealed a total of 394 differential expressed genes (DEGs) by pairwise comparisons among 3 groups. The flesh quality-specific differences at the transcriptional level were not only related to fat accumulation, but also affected lipids, proteins and carbohydrates biosynthesis and metabolisms. Functional enrichment analysis showed that response to stimulus, development process and signal transduction were also enriched within these DEGs. Our findings suggest that both HSD and LSD could lead to muscle fat infiltration, anti-oxidative inhibition, and lower expressions of immune factors, thereby obtaining higher fat deposition and lower disease resistance. In summary, C. idellus cultured at medium stocking density exhibited a higher muscle quality and healthier condition than those reared under crowding stress or at extreme low-stocking density.