Integrative Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms Underlying Hepatic Differences Between Zaozhuang Heigai Piglets and Duroc×Landrace×Yorkshire Piglets

Piglets weaning is a critical developmental stage marked by significant metabolic and inflammatory challenges. The hepatic responses during this period may differ among pig breeds with distinct genetic backgrounds. To explore the phenotypic and molecular differences in the livers between the Zaozhuang Heigai (HG) pig and Duroc×Landrace×Yorkshire (DLY) piglets and elucidate the regulatory mechanisms of genetic background on liver function, five 35-day-old piglets from each breed were selected. Body weight and liver coefficients were measured; histological features of liver sections were observed, and the transcriptome and metabolome of the liver were determined using mRNA sequencing and non-targeted metabolomics analysis. The results showed that HG piglets had significantly lower body weight (p < 0.01) and slightly higher liver coefficients than DLY piglets. Histological examination revealed that the hepatic lobule structure was intact in both breeds, while mild hepatic congestion was observed in some DLY piglets. Transcriptome analysis identified 429 differentially expressed genes (DEGs) with criteria of FDR adjusted p-values < 0.01 and |log2(Fold Change)| > 1, and they were significantly enriched in oxidoreductase activity, peroxisome proliferator-activated receptor (PPAR) signaling, and arachidonic acid metabolism pathways. Metabolome analysis identified 169 differentially expressed metabolites (DEMs) with criteria of p < 0.05, VIP > 1, and |log2(Fold Change)| > 1, and they were significantly enriched in nucleotide metabolism, arginine biosynthesis, and arachidonic acid metabolism pathways. Integrative analysis of DEGs and DEMs showed that arachidonic acid metabolism was the common pathway. Within this pathway, key genes (GPX3, ALOX5, and CBR3) were significantly associated with specific metabolites (15-deoxy-PGJ2 and phosphatidylcholines) (FDR adjusted p < 0.05), suggesting a gene–metabolite interaction network that coordinates inflammatory regulation and oxidative stress. These findings provide molecular evidence for breed-specific hepatic metabolic regulation during the weaning period and are therefore conducive to the management of weaned piglets and the investigation of local pig characteristics.