Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle

The genetic mechanisms controlling residual feed intake (RFI), a measure of feed efficiency in beef cattle, is still largely unknown. Here we performed global gene expression sequencing or RNA sequencing in beef cattle to identify differentially expressed genes and their functional roles related to RFI. The global RNA sequencing was conducted on liver samples that were collected from Angus, Charolais, and Kinsella Composite (KC) steers at slaughter. On average, the next generation RNA sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. The study identified 72, 41, and 175 genes that were expressed differently in Angus, Charolais, and KC, respectively. Most of the differentially expressed genes were breed-specific while five of them were common across the three breeds, with four out of the five genes being downregulated or less expressed in low RFI steers of all three breeds. The differentially expressed genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds. The results will not only help understand the biology of feed efficiency but also enable the development of gene based prediction tools to select more efficient beef cattle.