Transcriptomic Analyses Reveal Intestine and Liver Responses of Large Yellow Croaker (Larimichthys crocea) to Plant Protein Diet

Abstract

The utilization of plant protein in aquafeeds to reduce dependence on fishmeal has become an important strategy for improving the sustainability of marine aquaculture. This study investigated the effects of low-fishmeal plant protein diets on growth performance and gut–liver molecular responses in large yellow croaker. A total of 2,048 fish were fed two diets for 206 days: a commercial-like control diet containing 280 g/kg fishmeal (C group) and a low-fishmeal diet containing 100 g/kg fishmeal with increased inclusion of plant protein sources (P group). Growth trials indicated that fish in the C group had significantly higher weight gain rate and specific growth rate than those in the P group (p < 0.001). Transcriptomic analysis identified 546 and 724 differentially expressed genes (DEGs) in the hindgut and liver, respectively. Hindgut DEGs were mainly enriched in pathways associated with lipid metabolism, immune responses, and signal transduction, whereas liver DEGs were primarily involved in lipid metabolism, immune regulation, and apoptosis. Several pathways, including fat digestion and absorption, complement and coagulation cascades, taurine and hypotaurine metabolism, antigen processing and presentation, and cytokine–cytokine receptor interaction, were enriched in both tissues, suggesting coordinated gut–liver regulation. Representative genes involved in lipid metabolism and immune regulation, including apob, scarb1, c3, b2m, and ccr9, exhibited tissue-specific and coordinated expression changes. PPI network analysis further identified c3, scarb1, vwf, and apob as key regulatory nodes potentially involved in coordinated metabolic and immune adaptation. Collectively, these findings provide new insights into the molecular mechanisms underlying gut–liver adaptation to plant-based diets in marine fish.