Transcriptome Profiling of Rumen Epithelial Tissues of Beef Cattle Differing in Residual Feed Intake

The molecular mechanisms of feed efficiency in cattle are largely unknown. This study aimed to investigate the differences in gene expression and determine the cellular and molecular functions of genes in the rumen epithelial tissue of beef cattle differing in feed efficiency. Residual feed intake (RFI) of 175 Hereford x Angus steers was measured using a GrowSafe system. The transcriptome of the rumen epithelium from 5 of the most efficient (low RFI) and 5 of the most inefficient (high RFI) steers were obtained using RNA-seq and differential gene expression analysis was conducted using edgeR software. Core functions of the rumen transcriptome were analyzed using Ingenuity Pathway Analysis software (IPA). The rumen epithelial transcriptome consisted of 16,745.3 ± 327.36 (mean ± SD; N=10) transcribed genes with a core function of cellular growth and proliferation. There were 5 rumen epithelial genes that were significantly differentially expressed between low- and high- RFI steers based on a false discovery rate (FDR) of less than 0.05. Efficient individuals showed lower expression of IGFBP2, but had higher expression of PLET1, CLDN17, GPX2 and SLC26A9. Functional analysis of CLDN17 showed its potential involvement in feed efficiency through transport of anions, possibly of volatile fatty acids. Our results also indicate that the rumen epithelium of efficient individuals is adapted to reduce oxidative stress and acidic injury. Understanding how host gene expression profiles are associated with RFI could potentially lead to identification of biomarkers for selection of highly feed efficient cattle.