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

Abstract

The genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE 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.

Figure 1

Venn diagrams showing: (a) overlap of expressed genes (>1CPM in ≥6 samples) in the three studied breed populations; (b) overlap of differentially expressed genes (DE genes) in the three studied breed populations; (c) overlap of biological functions enriched by DE genes identified in the three studied breed populations.

Figure 2

Expression profile (log₂ (Fold-change)) in low-RFI steers of the five differentially expressed (DE) genes common across all three breeds.

Figure 3

Metabolic process regulatory gene network showing differentially expressed (DE) genes involved in the different lipid metabolic processes and their predicted activation or deactivation levels in Angus low-RFI steers.

Figure 4

Metabolic process regulatory gene network showing differentially expressed (DE) genes involved in the different lipid metabolic processes and their predicted activation or deactivation levels in Charolais low-RFI steers.

Figure 5

Metabolic process regulatory gene network showing differentially expressed (DE) genes involved in the different lipid metabolic processes and their predicted activation or deactivation levels in KC low-RFI steers.