Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake

Abstract

Feed efficiency is an economically important trait in beef production. It can be measured as residual feed intake. This is the difference between actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. DNA-based marker-assisted selection would help beef breeders to accelerate genetic improvement for feed efficiency by reducing the generation interval and would obviate the high cost of measuring residual feed intake. Although numbers of quantitative trait loci and candidate genes have been identified with the advance of molecular genetics, our understanding of the physiological mechanisms and the nature of genes underlying residual feed intake is limited. The aim of the study was to use global gene expression profiling by microarray to identify genes that are differentially expressed in cattle, using lines genetically selected for low and high residual feed intake, and to uncover candidate genes for residual feed intake. A long-oligo microarray with 24 000 probes was used to profile the liver transcriptome of 44 cattle selected for high or low residual feed intake. One hundred and sixty-one unique genes were identified as being differentially expressed between animals with high and low residual feed intake. These genes were involved in seven gene networks affecting cellular growth and proliferation, cellular assembly and organization, cell signalling, drug metabolism, protein synthesis, lipid metabolism, and carbohydrate metabolism. Analysis of functional data using a transcriptional approach allows a better understanding of the underlying biological processes involved in residual feed intake and also allows the identification of candidate genes for marker-assisted selection.

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake

“…Owing to an insufficient number of tissues being sampled, the association between CNV and mRNA expression was not analyzed in this study. A previous study in cattle reported that the expression of most genes upregulated in low RFI animals was stimulated by the MAPK pathway, which is involved in cellular growth and proliferation (Chen et al, 2011). Serão et al (2013) noted that the MAPK signaling pathway was over-represented among genes harboring SNPs associated with feed efficiency traits (RFI, FI, ADG, and efficiency of gain) in beef cattle.…”

Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle

“…Homeostasis requires more energy expenditure for animal maintenance and it involves a series of metabolic pathways, mainly related to ion transport, energy metabolism, and protein turnover . In addition, GWAS have also pointed to ion transport as one of the main mechanisms related to feed efficiency (Serão et al, 2013;Santana et al, 2014); global expression profile analysis in high and low feed efficiency animals showed a regulator of ion transport as one of the differentially expressed genes in Angus cattle (Chen et al, 2011).…”

Visceral organ weights, digestion and carcass characteristics of beef bulls differing in residual feed intake offered a high concentrate diet

“…These discrepanacies in energetic efficiency of metabolic processes within tissues may explain the absence of an effect of RFI on visceral organs weights despite a reduced DMI of the low RFI bulls in the current study. Indeed, Chen et al (2011) found differential hepatic gene expression between high and low RFI animals in processes involved in carbohydrate metabolism, lipid metabolism and protein synthesis among other processes. Similarly, Connor et al (2010) found that steers exhibiting compensatory growth and greater efficiency of ADG than control animals, had increased expression of hepatic genes involved in processes such as cellular metabolism, oxidative phosphorylation and glycolysis.…”