Swine

Integrative metabolomic-genomic analyses uncover key regulators of metabolism in growing Duroc male pigs

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Abstract

Understanding the genetic architecture underlying complex traits is a major challenge in livestock breeding, especially for traits like efficiency and resilience that are difficult to define and measure. This study aimed to identify genetic regulators of pig metabolism by integrating metabolomic and genomic data, using a phenomics approach. A total of 290 growing male pigs from a male Duroc line, divergent for feed efficiency, were blood sampled. Plasma was obtained and analyzed using an untargeted metabolomics platform (Metabolon), quantifying ~700 metabolites. All animals were genotyped using a medium-density SNP panel. After quality control, 274 animals, 592 metabolites, and 33.285 SNPs were retained. Genomic heritability estimates were obtained, and genome-wide association studies (GWAS) were conducted using the GEMMA tool. A Bonferroni correction (α = 0.05) was applied to determine genome-wide significance. Heritability estimates (±s.e.) ranged from 0.00 to 0.83 ± 0.08, with a mean of 0.16 (s.d. = 0.14). Notably, 32% of metabolites showed heritability estimates ≥ 0.20, indicating moderate to strong genetic control. GWAS identified significant associations (P < 0.05/33.285) for 101 metabolites across all Sus scrofa chromosomes (SSC) except SSC17. For 88 metabolites, one major metabolite QTL (mQTL) was identified, while two or more loci were detected for the remaining metabolites. The mean percentage of phenotypic variance explained by individual top-associated SNPs was 15.34% ± 8.38. Some mQTLs were shared among multiple metabolites; for example, two loci on porcine chromosomes 2 and 14 were associated with ten or more metabolites, distributed across different biochemical classes and biological super-pathways. Functional annotation of associated loci revealed enrichment for genes encoding enzymes, transporters, and regulatory proteins directly involved in the metabolism of the associated compounds. These findings confirm that circulating metabolite levels are under substantial genetic control and demonstrate the value of molecular phenotypes in revealing the genetic basis of physiological processes. This integrative metabolomic-genomic study uncovered key regulators of pig metabolism and supports the use of high-throughput metabolomics to discover biomarkers to implement precision breeding (and feeding) strategies, enhancing selection for traits related to efficiency and robustness, and contributing to more sustainable pig production systems. Acknowledgments: This study received funding from the European Union's Horizon Europe research and innovation programme under grant agreement No. 101059609 (Re-Livestock project).

Keywords: 2026

How to Cite:

Bovo, S., Bolner, M., Holl, J., Valente, B., Lewis, C., Schiavo, G., Bertolini, F. & Fontanesi, L., (2026) “Integrative metabolomic-genomic analyses uncover key regulators of metabolism in growing Duroc male pigs”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285616. doi: https://doi.org/10.31274/wcgalp.23755

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