Post-Weaning Blood Transcriptomic Differences Between Yorkshire Pigs Divergently Selected for Residual Feed Intake

Improving feed efficiency (FE) of pigs by genetic selection is of economic and environmental significance. One measure of feed efficiency is residual feed intake (RFI). Currently, the molecular mechanisms underlying RFI are largely unknown. In this study, we explored whether differences exist in the global gene expression profiles of peripheral blood of 35-42 day-old pigs with extremely low (more efficient) and high RFI from two lines that were divergently selected for RFI, to use such information to explore the molecular basis of RFI differences, and to initiate development of predictive biomarkers for RFI. We identified 454 differentially expressed genes (DEGs) (q ≤ 0.05) between the low (n = 15) and high (n = 16) RFI animals by using RNAseq. We validated 24 of 37 selected DEGs by RT-qPCR. The 1972 DEGs (q ≤ 0.15) significantly overlapped with genes associated with several diseases, including hyperphagia, eating disorders and mitochondrial diseases (q < 1E-05). Gene Ontology term overrepresentation analysis suggested differences in mitochondrial and proteasomal activities, small molecule biosynthetic process, and signal transduction between the two RFI lines and provided new insights into the molecular basis of RFI in pigs. A weighted gene co-expression network analysis identified four co-expression modules differentially expressed between the low and high RFI groups, and there was significant overlap between cluster membership and DEGs. These DEGs and representative genes from co-expression modules that were associated with RFI phenotype provided a preliminary list for developing predictive biomarkers for RFI in pigs.

Supported by USDA- NIFA-AFRI-2011-68004-30336.