Background: Fat metabolism in pigs is controlled by tissue-specific molecular mechanisms that ultimately affect growth performance and meat quality. Understanding how epigenetic modifications interact with gene expression across key metabolic and fat-depositing tissues is essential for identifying regulatory processes and potential biomarkers to improve pork quality traits. Therefore, this study aimed to elucidate tissue specific epigenetic regulation of fat metabolism by integrating DNA methylation and gene expression profiles from liver, backfat, and loin (longissimus dorsi) tissues at two physiologically developmental stages (10 and 26 weeks), representing the early post-weaning growth phase and near-market weight, respectively. By explicitly comparing these ages and tissues, the study was designed to capture the transition from muscle-dominated growth to increased lipid deposition and to identify tissue- and stage-specific regulatory signatures that may serve as biomarkers for pork quality.
Results: Genome-wide DNA methylation exhibited weak clustering by tissue, whereas gene expression showed clear tissue separation. The liver harbored fewer genes with differential methylation across stage and tissue but a greater number of genes with differential expression than backfat and loin, suggesting distinct regulatory modes. Integrative analysis of the overlap genes between methylation and expression signals highlighted epigenetically mediated regulation of extracellular matrix organization, lipid metabolism, and muscle development pathways. Furthermore, weighted gene co-expression network analysis revealed distinct tissue-specific correlations between co-methylated and co-expressed modules, with enrichment in cholesterol biosynthesis, muscle contractility, and extracellular matrix remodeling. Together, these findings suggest that methylation changes are more subtle than transcriptional shifts, yet they are aligned with key functional pathways, consistent with a role for methylation as a fine-tuning mechanism that shapes tissue-specific transcriptional networks during growth.
Conclusions: Across liver, backfat, and loin, DNA methylation modulates transcriptional programs in a tissue-dependent manner, prioritizing pathways central to lipid handling, extracellular matrix remodeling, and muscle function. This integrated multi-omics framework highlights candidate epigenetic markers and regulatory modules with potential utility for improving pork quality traits through selection or management strategies.
Background: Colostrum is recognised as the "golden elixir of health" due to its optimal chemical, immunological and nutraceutical properties for newborns, but little is known about its nature in the pig. This study aims to provide a multi-omics characterisation of pig colostrum from different parities (gilts, n = 7, second, n = 7 and mature, n = 6 sows) to identify the most relevant bioactive compounds associated with piglet survival and average daily gain (ADG) and faecal microbiota till d 6 and d 24.
Results: Nine hundred and fifty metabolites (108 chemically confirmed) and 71 fatty acids (FAs) were characterised in colostrum. Parity class was the main driver for piglet survivability (P < 0.001; highest in second parity), metabolomics (R2 = 0.97; Q2 = 0.52; > 200 discriminated metabolites) and lipidomic profile (22 discriminated FAs) and piglet faecal microbiota (beta diversity P < 0.05 at d 6 and d 24). Colostrum composition allowed clustering for piglet mortality from d 0 to d 6 (Q2 > 0.50). Mortality classes at d 6 were discriminated by 177 metabolites and 2 FAs and 248 metabolites and 21 FAs at d 24. At both timepoints a higher abundance of C18:2 8trans,10cis discriminated for lower mortality (importance = 1 for d 6 and 0.34 for d 24). Pathway analysis at d 6 and d 24 indicated arginine biosynthesis and alpha-linoleic acid metabolism as most enriched metabolism in swine colostrum related to higher survivability. The multi-omics integration analysis revealed that a higher faecal abundance of Lachnospiraceae_FCS020, Holdemania, Roseburia, and a higher colostrum abundance of C18:2 8trans,10cis, and the C18:1 5trans and salicylic acid as metabolites were the most associated with a lower mortality. The ADG classes d 0-24 were discriminated by 151 metabolites and 33 FAs. Higher ADG (240 g/d) was discriminated by colostrum vitamin E, histidine, and branched-chain amino acids (VIP score > 1), while L-kynurenine and gamma-aminobutyric acid were linked to lower growth, suggesting maternal stress.
Conclusion: This study confirms the importance of parity order in shaping colostrum composition and identifies several bioactive compounds, some parity-dependent and others parity-independent, that may be associated with improved piglet survival and gut microbiota maturation. The findings may also support the development of next-generation artificial colostrum supplements.
Background: The transition period is a critical phase for the sow due to physiological changes and nutritional requirements. A diet balanced in energy and amino acid (AA) content could improve reproductive performance, colostrum quality and piglets' growth. This study evaluated the efficacy of a transition diet (TRT) with higher energy (12.97 MJ/kg of metabolizable energy (ME)) and SID lysine (Lys; 0.85%), compared to a standard (CO) diet (12.33 MJ/kg of ME and 0.70% SID Lys), on the composition and quality of colostrum and on sow and piglet performance. The AA/SID Lys ratio was maintained in both diets. Sows (50 sows/group) were fed the CO or TRT diet from 6 d prepartum to d 4 postpartum. At farrowing, sow performance (50 sows/group) and piglet vitality (12 sows/group) were recorded, and colostrum (20 sows/group) was collected to analyze its composition and microRNAs. Piglet performances were collected d 6 and weaning (d 24).
Results: The diet did not affect sow feed intake, body condition score, backfat and muscle loss, nor farrowing duration and time interval between piglets. The TRT group had fewer stillbirths (P = 0.002). Piglets of TRT litters had higher body weight at d 24 (P = 0.032) and tended to have higher average daily gain from d 0 to d 24 (P = 0.080). Colostrum from the TRT group tended to be higher in somatic cell count (P = 0.07), higher in fat percentage (P = 0.036), and higher in C18:2 9cis,12cis, C18:4 6cis,9cis,12cis,15cis, C20:0, UDP-glucuronate and carnitine (P < 0.05); moreover, it had a lower concentration of citrate (P < 0.05). The 208 microRNAs were detected in colostrum, 13 of which were differentially expressed (P < 0.05). The TRT group had a higher ssc-miR-143-3p expression, which is associated with increased phagocytosis and reduced inflammation and oxidative stress. This, together with the increase in fat and specific metabolites related to energy metabolism, could potentially benefit piglet performance.
Conclusion: These results suggest that the TRT diet improves sow parturition and lactation performance by modifying sow energy metabolism and colostrum quality. This highlights the importance of a properly designed transition diet for sows.
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