Replacement of Soybean Meal with Fermented Dried Tomato Pomace Modulates Immune Responses, Antioxidant Gene Expression, and Meat Quality in Boer Goats: Insights from Hepatic Transcriptomics

This study evaluated the effects of replacing soybean meal with fermented dried tomato pomace (FDTP) on biochemical, immune, and antioxidant responses, meat quality, and hepatic transcriptomic profiles in Boer goats. Twenty-four male goats were assigned to a control diet or diets in which FDTP replaced 33.33% (T1), 66.66% (T2), or 100% (T3) of soybean meal for 60 days (n = 6). Serum biochemical parameters, total immunoglobulin, and alternative complement hemolytic activity were unaffected, whereas lysozyme activity increased linearly with FDTP replacement. FDTP increased muscular SOD1 expression and altered cytokine expression in a tissue-specific manner, including increased IL10 and reduced IL1B and TNFα expression in selected tissues. In gastrocnemius muscle (n = 3), T2 had higher collagen content and lower cooking loss than the control and T3, whereas T3 had higher drip loss than T2; selected textural properties were also altered. During refrigerated storage, lipid oxidation was affected by storage day but not by treatment or the treatment × day interaction. T2 was selected post hoc for exploratory hepatic transcriptomic comparison with the control (n = 5). Among 587 DEGs, significantly enriched KEGG pathways involved metabolism and biotransformation, including steroid hormone biosynthesis, retinol metabolism, bile secretion, xenobiotic metabolism, and pentose and glucuronate interconversions. In addition to the enriched pathways, PI3K–Akt, MAPK, NF-κB, and cytokine–cytokine receptor pathways contained DEGs related to metabolic, stress, and immune responses. Overall, FDTP replacement was associated with changes in selected immune and meat-quality traits and with hepatic transcriptional responses predominantly related to metabolic and biotransformation processes.