Multi-omics insights into ferroptosis and muscle yellowing–related quality defects in grass carp (Ctenopharyngodon idellus)

Muscle yellowing is an emerging quality defect in farmed grass carp, yet its chemical and molecular regulation remain insufficiently understood. Here, we integrated transcriptomics, proteomics and metabolomics with targeted quality assessments to compare normal (N) and yellowish (Y) dorsal muscles in grass carp. Yellowish muscle showed marked discoloration, with a significant decreases in lightness (L*: 57.57 vs. 39.76) and an increase in yellowness (b*: 1.53 vs. 3.84), accompanied by an overall decline in eating quality. Multi-omics profiling identified 4,601 differentially expressed genes, 937 differentially abundant proteins, and 120 differential metabolites, and the three datasets consistently converged on pathways related to oxidative stress, ferroptosis, and dysregulated lipid metabolism. Biochemical indices further supported intensified oxidative damage and weakened antioxidant capacity in yellowish muscle, indicating disrupted redox homeostasis that favors lipid peroxidation. Odor- and taste-related fingerprints, assessed using an electronic nose and electronic tongue, clearly separated the N and Y groups, suggesting systematic alterations in volatile and taste-active compounds during yellowing. Moreover, amino acid profiling indicated reduced nutritional value in yellowish muscle, reflected by decreased levels of multiple amino acids. Together, these findings link muscle yellowing with oxidative stress–driven lipid peroxidation and ferroptosis-associated regulation, providing mechanistic insight and potential biomarker candidates for quality monitoring and targeted mitigation in grass carp production. • Muscle yellowing impaired sensory quality and nutritional attributes of grass carp. • Integrated omics revealed oxidative stress and ferroptosis as primary drivers of discoloration. • Altered lipid metabolism and phospholipid remodeling contributed to texture and flavor defects. • Iron overload and lipid peroxide accumulation intensified yellow pigmentation. • Lipofuscin was identified as a key pigment associated with yellowish muscle.