A multi-omic atlas of the maternal-fetal dyad reveals metabolic stratification and prenatal signatures potentially relevant to meat quality development.

Meat quality is influenced by non-lipid small molecules, yet prenatal metabolic organization remains unclear. Here, we constructed a high-resolution atlas of flavor- and color-related metabolism using a maternal-fetal goat dyad. We integrated full-spectrum metabolomics, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), and full-length transcriptomics to profile longissimus dorsi muscle (LDM) and leg biceps femoris muscle (LM). Multi-omic analysis revealed a dominant two-axis pattern, with many metabolites showing higher abundance in maternal than fetal muscle and in LDM than LM. Maternal LDM was enriched in inosine-5'-monophosphate and citric acid, accompanied by higher pooled AMPD1 transcript abundance and a maternal-associated transcript abundance pattern of TCA-cycle-related genes. In contrast, fetal LM accumulated inosine and hypoxanthine. Although fetal muscles showed lower overall amino acid reserves, lysine and glutamate were locally enriched in superficial fast fibers. Histidine dipeptides showed similar superficial enrichment, providing insight into prenatal metabolic features potentially relevant to later meat quality development.