Identification of genes expressed in the liver transcriptome of Holstein-Friesian and Charolais steers divergent in residual feed intake across three dietary phases

The identification of genes implicated in the divergence of residual feed intake (RFI) and their inclusion in genomic assisted breeding programmes may enable rapid, cost-effective selection of low RFI cattle. However, markers for RFI used for genomic selection must be robust across breed and the various diets that may be offered to beef cattle. The objective of this study was to identify genes associated with RFI divergence in hepatic tissue from two cattle breeds over varying dietary stages using differential gene expression analysis and gene co-expression analysis. Using RNA-Seq, hepatic differential gene expression of Charolais (CH) and Holstein-Friesian (HF) steers divergent in RFI was investigated. Animals were offered three contrasting diets, high-concentrate (H1), zero-grazed grass (ZG) and returned to a high-concentrate diet (H2). Liver biopsies were collected at the end of each dietary phase and RNA-Seq libraries were generated for animals most divergent in RFI (n=43 low RFI, n=47 high RFI). On average, 29.1 million reads were obtained per sample, 97% of generated reads had a quality score greater than 30 and 92% of reads mapped uniquely to the reference genome (UMD3.1). At a false discovery rate of 2, 18 differentially expressed genes (DEGs) were identified across diet for CH and 21 DEGs were observed across diet for HF. Agouti signalling protein(ASIP)was differentially expressed across two dietary phases for CH. No gene was differentially expressed in more than one diet for HF. Gene co-expression analysis was carried out using weighted gene co-expression network analysis. Fifteen modules of genes with similar expression patterns across breed and diet were identified. However, none of these modules were significantly correlated with RFI across diet. Our results highlight the difficulty in identifying robust biomarkers for RFI that are applicable across both diet and breed for beef cattle.