Small networks of expressed genes in the whole blood and relationships to profiles in circulating metabolites provide insights in inter-individual variability of feed efficiency in growing pigs

Transcriptomic dataset was obtained from NCBI’s Gene Expression Omnibus (GEO) Subserie accession number GSE70838 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70838).The metabolomic dataset was retrieved in Jegou et al. [14]. Phenotypic traits and fatty acid composition in plasma are are deposited in the publicly available repository at https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/TM2ANC.The adjacency matrix is available at https://data-access.cesgo.org/index.php/s/YPz0J2ItxIEuN5M.We provide R notebooks detailing the analysis https://github.com/cjuigne/multiomics_and_feed_efficiency; Background: Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs. Results: The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (1H-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co-expression network was built from the transcriptomics dataset, resulting in 33 modules of coexpressed molecular probes. The eigengenes of eight of these modules were significantly (P ≤ 0.05) or tended to be (0.05 < P ≤ 0.10) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes. They were also generally associated with growth rate and percentage of lean mass. In the network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The profiles in circulating metabolites and fatty acids of plasma were summarized by weighted linear combinations using a dimensionality reduction method. Close association was notably found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of omega-3 fatty acids in plasma. Conclusion: These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits.