Transcriptome Analysis Revealed the Affecting Mechanism of Two Diets, Trash Fish or Compound Feed, on Flesh Quality of Largemouth Bass (Micropterus salmoides)

Abstract

This study revealed the affecting mechanism of trash fish (TF) and compound feed (CF) on the flesh quality of largemouth bass (Micropterus salmoides) based on muscle transcriptome. Largemouth bass weighing 75.0 ± 0.1 g were given TF or CF for a period of 12 weeks. The CF group presented significantly higher feed efficiency (FE) than the TF group (p < 0.05), while there was no significant difference in specific growth rate (SGR) between the two groups (p > 0.05). A total of 604 differentially expressed genes (DEGs) meeting the significance criteria of p-value < 0.05 and |log2foldchange| > 1 were identified in the muscle transcriptome analysis. Compared to the TF group, 145 DEGs were downregulated, and 459 DEGs were upregulated in the CF group. Enrichment analysis of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed significant enrichment of 401 GO terms and 13 pathways, respectively. In the CF group, there was a notable increase in gene expression in pathways such as arachidonic acid (AA) metabolism, protein processing in the endoplasmic reticulum, cholesterol metabolism, MAPK, and focal adhesion, while there was a decrease in pathways like purine metabolism, apoptosis, glycolysis/gluconeogenesis, and PPAR signaling. Real-time fluorescence quantitative PCR results indicated decreased expression of tni (troponin I, fast skeletal muscle-like) and increased expression of stni (troponin I, slow skeletal muscle-like), ftni (troponin I, fast skeletal muscle), mustn1b (musculoskeletal, embryonic nuclear protein 1b), actn2b (alpha-actinin−2), and hspb1 (heat shock protein [HSP] beta 1) in the CF group compared to the TF group. Overall, according to transcriptomics, replacing TF with CF altered the gene expression related to meat and the associated signaling pathways, leading to the meat quality improvement for largemouth bass.