Candidate genes, metabolites and biological pathways associated with residual feed intake and carcass quality in beef cattle

The main objective of this study was to identify genes, DNA variants and plasma metabolites associated with residual feed intake (RFI) in beef cattle. In the first study, a total of 117 SNPs were selected and genotyped in 531 steers at the University of Alberta. The population was split into a discovery and validation population and multiple marker association analyses were performed in the discovery, validation and combined populations using ASReml. Twenty two SNPs were associated (P < 0.05) with RFI in the discovery population and 7 (of the 22) were also significant (P < 0.05) in the validation population. Twenty five SNPs were associated with RFI (P < 0.05) in the pooled population. A gene network analysis indicated that the biological processes associated with the significant genes included lipid, glucose, protein and steroid metabolism, growth, energy utilization, and regulation of DNA transcription and translation. The second study was an association analysis using the 117 SNPs and indicated that 7 were associated with various carcass quality traits (p ≤ 0.005) in the same population. A third association analysis was performed using steers at the University of Guelph, as the discovery population, to identify blood metabolites associated with RFI. Blood samples were collected at 3 periods with period 1, 2 and 3 corresponding to week 2, 6 and 9 into the feeding period respectively. Two, ten and three metabolites were significantly associated with RFI (P < 0.05) in period 1, 2 and 3 and accounted for 36%, 74% and 52% of the variation respectively. A validation analysis was performed using steers at the University of Alberta as the validation population. The results indicated that 3 metabolites were significantly associated with RFI in both discovery and validation populations accounting for 32.8% of the variation in the validation population. A metabolic network analysis indicated that the biological pathways associated with the metabolites included AMPK signaling, growth hormone signaling, lipid and energy metabolism and cholesterol metabolism. The genes, metabolites, biological networks and the biological pathways help contribute to a better understanding of the physiological processes influencing RFI and carcass quality in beef cattle.