Multi-omics analysis reveals the effects of prenatal nutrition on carcass-related tissues in beef cattle

Abstract

Abstract This study evaluated the long-term metabolic effects of prenatal nutrition in Nellore bulls. Pregnant cows ( n  = 126) received mineral supplementation only (NP), protein–energy supplementation during the last trimester (PP), or supplementation throughout pregnancy (FP). At slaughter, longissimus (muscle and meat) and subcutaneous fat samples from the offspring were collected for transcriptomics and metabolomics analyses. Data were reduced using Weighted Gene Co-expression Network Analysis, followed by functional enrichment, and then integrated via Spearman’s correlations and holistic pathway analysis. Distinct molecular patterns emerged across prenatal nutrition treatments, although all groups influenced energy metabolism and cellular processes. The NP group was strongly associated with protein and lipid metabolism, highlighted by PPAR and sphingolipid signaling pathways, and key hub components including CNOT4 and tryptophan. In contrast, PP and FP groups were more closely linked to immune function, stress resilience, with enrichment of NF-kB signaling, cortisol synthesis, and hub components including TIE1 , YWHAZ , carnitine, and glutaconylcarnitine. Shared transcriptome–metabolome modules between groups displayed inverse correlations, suggesting potential antagonistic effects driven by maternal diet. Overall, these results indicate that prenatal nutrition shapes key metabolic processes in muscle, meat, and fat, offering insights to enhance meat quality and production through maternal feeding strategies.