RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

BMC Genomics

Research Article

G. Mazzoni¹  M. S. Salleh¹  P. Lund²  H. N. Kadarmideen³  P. Løvendahl⁴  J. K. Höglund⁴  D. W. Olijhoek⁵ 

[1] Animal Breeding, Quantitative Genetics and Systems Biology Group, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870, Frederiksberg C, Denmark;Department of Animal Science - Animal Nutrition and Physiology, Aarhus University, AU Foulum, DK-8830, Tjele, Denmark;Department of Bio and Health Informatics, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark;Department of Molecular Biology and Genetics - Center for Quantitative Genetics and Genomics, Aarhus University, AU Foulum, DK-8830, Tjele, Denmark;Department of Molecular Biology and Genetics - Center for Quantitative Genetics and Genomics, Aarhus University, AU Foulum, DK-8830, Tjele, Denmark;Department of Animal Science - Animal Nutrition and Physiology, Aarhus University, AU Foulum, DK-8830, Tjele, Denmark;

关键词: RNA-Seq;    Feed efficiency;    Residual feed intake;    Differentially expressed genes;    Pathways;    Dairy cattle;   

DOI  :  10.1186/s12864-017-3622-9

 received in 2016-09-29, accepted in 2017-03-11,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE.ResultsThe bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450.ConclusionWe used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular pathways. The DEGs that were identified were the CYP’s and GIMAP genes for the Holstein and Jersey cows, respectively, which are related to the primary immunodeficiency pathway and play a major role in feed utilization and the metabolism of lipids, sugars and proteins.

【 授权许可】

CC BY   
© The Author(s). 2017