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Liver transcriptome profiling of beef steers with divergent growth rate, feed intake or metabolic body weight phenotypes.

Average daily gain (ADG) and daily dry matter intake (DMI) are key determinants of beef industry profitability. These traits together with metabolic body weight (MWT) are combined as component traits to calculate residual feed intake (RFI), a common measure of feed efficiency in beef cattle. Recently, there have been significant efforts towards molecular genetic characterization of RFI through transcriptomic studies in different breeds and tissues. However, molecular mechanisms of RFI component traits still remain predominately unexplored. Therefore, in the current study we investigated the hepatic transcriptomic profiles and their associations with ADG, DMI and MWT in Angus, Charolais, and Kinsella Composite (KC) populations through global RNAseq analyses. In each population and for each trait, 12 steers with extreme phenotypes (n = 6 low and n = 6 high) were analyzed for differential gene expression. These animals were from 20 beef steers of each Angus, Charolais and KC breed population that were initially selected for a transcriptome study of residual feed intake (RFI). At a false discovery rate (FDR) < 0.05 and fold change ≥ 1.5, we identified 123, 102 and 78 differentially expressed (DE) genes between high and low-ADG animals of Angus, Charolais and KC populations, respectively. For DMI, 108, 180 and 156 DE genes were identified between high and low-DMI from Angus, Charolais and KC populations, respectively, while for MWT, 80, 82 and 84 genes were differentially expressed between high and low-MWT animals in Angus, Charolais and KC populations, respectively. The identified DE genes were largely breed-specific (81.7% for ADG, 82.7% for DMI, and 83% for MWT), but were largely involved in the same biological functions across the breeds. Among the most enriched biological functions included metabolism of major nutrients (lipid, carbohydrates, amino acids, vitamins and minerals), small molecule biochemistry, cellular movement, cell morphology and cell-to-cell signalling and interaction. Notably, we identified multiple DE genes that are involved in cholesterol biosynthesis, and immune response pathways for the three studied traits. Thus, our findings present potential molecular genetic mechanisms and candidate genes that influence feed intake, growth, and metabolic body weight of beef cattle.