Dietary Lepidium meyenii Supplementation Is Associated with Hepatic Transcriptomic and Targeted DNA Methylation Changes in Pigs

Background: Lepidium meyenii Walp. (maca) is a plant-derived feed supplement rich in bioactive compounds such as macamides, macaenes, glucosinolates, and polyphenols. In this study, it was selected as a potential natural functional feed additive based on its bioactive phytochemical composition, reported metabolic properties, and previously observed effects on porcine cells. However, its molecular effects in livestock remain poorly characterised. This study investigated hepatic molecular responses to dietary maca supplementation in pigs using transcriptomic analysis followed by DNA methylation, promoter polymorphism, and protein analyses to explore the mechanisms underlying the observed transcriptional changes. Methods: Female pigs were assigned to two groups fed a diet supplemented with 1% maca powder (E) or a control diet (C). Liver samples were analysed using RNA sequencing and qPCR validation of selected genes. DNA methylation, promoter variants, and TUBA4A protein abundance were assessed using pyrosequencing, Sanger sequencing, and Western blotting, respectively. Results: RNA-seq identified 104 differentially expressed genes (DEGs) after DESeq2 analysis with intensity difference filtering. qPCR validated the differential expression of INHBE, PPP1R3C, PPP1R3B, TUBA4A, and GCK. Gene Ontology enrichment analysis indicated the over-representation of terms related to extracellular matrix organisation, collagen-containing structures, response to transforming growth factor beta, and glycogen biosynthetic processes. Methylation analysis revealed no significant methylation changes in GCK, INHBE, PPP1R3C, or TUBA4A after FDR correction, whereas PPP1R3B showed significant differences at seven CpG sites. Promoter polymorphisms were identified in PPP1R3C and TUBA4A, but genotype frequencies did not differ between groups. Additionally, TUBA4A protein abundance was not altered. Conclusions: Dietary maca supplementation was associated with moderate hepatic molecular changes, including alterations in genes and pathways related to glycogen metabolism and extracellular matrix organisation. Maca may represent a promising natural feed supplement for pigs, although further studies are needed to confirm its efficacy and practical applicability.