Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes

Abstract

BackgroundEfficiency of feed utilization is important for animal production because it can reduce greenhouse gas emissions and improve industry profitability. However, the genetic basis of feed utilization in livestock remains poorly understood. Recent developments in molecular genetics, such as platforms for genome-wide genotyping and sequencing, provide an opportunity to identify genes and pathways that influence production traits. It is known that transcriptional networks influence feed efficiency-related traits such as growth and energy balance. This study sought to identify differentially expressed genes in animals genetically divergent for Residual Feed Intake (RFI), using RNA sequencing methodology (RNA-seq) to obtain information from genome-wide expression profiles in the liver tissues of Nelore cattle.ResultsDifferential gene expression analysis between high Residual Feed Intake (HRFI, inefficient) and low Residual Feed Intake (LRFI, efficient) groups was performed to provide insights into the molecular mechanisms that underlie feed efficiency-related traits in beef cattle. A total of 112 annotated genes were identified as being differentially expressed between animals with divergent RFI phenotypes. These genes are involved in ion transport and metal ion binding; act as membrane or transmembrane proteins; and belong to gene clusters that are likely related to the transport and catalysis of molecules through the cell membrane and essential mechanisms of nutrient absorption. Genes with functions in cellular signaling, growth and proliferation, cell death and survival were also differentially expressed. Among the over-represented pathways were drug or xenobiotic metabolism, complement and coagulation cascades, NRF2-mediated oxidative stress, melatonin degradation and glutathione metabolism.ConclusionsOur data provide new insights and perspectives on the genetic basis of feed efficiency in cattle. Some previously identified mechanisms were supported and new pathways controlling feed efficiency in Nelore cattle were discovered. We potentially identified genes and pathways that play key roles in hepatic metabolic adaptations to oxidative stress such as those involved in antioxidant mechanisms. These results improve our understanding of the metabolic mechanisms underlying feed efficiency in beef cattle and will help develop strategies for selection towards the desired phenotype.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1464-x) contains supplementary material, which is available to authorized users.

Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake

“…Current technologies allow the measurement of the expression of each gene in each tissue of an individual using, for example, RNA sequencing (RNA-seq). Recently an RNA-seq study reported that changes in the hepatic gene expression between efficient and inefficient Nelore cattle primarily appear to be related to metabolic processes underlying oxidative stress12. This study identified several differentially expressed (DE) genes involved in mitochondrial functions.…”

Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content

“…Fatty acid molecules are broken down to generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH2 co-enzymes are used in the electron transport chain [53]. Tizioto et al [54] performed DEG gene analysis between animals that showed high (inefficient) and low (efficient) residual feed intake from the same population used in this study, and indicated the metabolic processes that underlie oxidative stress are a primarily network related to lipid metabolism and energy required for maintenance. These authors also observed the important role of fatty acids in energy metabolism and mitochondrial action on lipid oxidation process similar to that reported in this study.…”

Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid

“…However, recent studies revealed a limitation of genome-wide association study (GWAS) to identify loci with significant effects on different populations of the same breed, since many discordant genomic regions have been identified [50]. Tizioto et al [51] observed DEG using RNA-seq method and also applied GWAS to identify genomic regions for feed efficiency in Nellore cattle. These authors found several biological mechanisms and attributed the differences in the candidate regions/genes to the specific modulation of mRNA.…”

“…Therefore, the production of the required information is essential and needed to improve the marketing of beef products. There are few studies about transcriptome in Zebu animals, in which [51] is the unprecedented as it is the first study of gene expression for beef feed efficiency in Bos indicus animals. Thus, it provides subsidies to improve the beef quality of Zebu cattle under tropical conditions, producing a healthier food for consumers.…”