Comparative transcriptome analysis reveals genes associated with variation in liver copper concentration in Polish Merino sheep

Abstract

Abstract Economic gain for sheep farmers is continually affected by incidences of copper intoxication and deficiency. This study assessed the ovine genome for differentially expressed genes (DEGs) influencing within-breed variation in hepatic copper content in Polish Merino sheep. To this end, we compared whole genome RNA sequence expression data from 12 female Polish Merino sheep liver samples (dataset 1) selected and grouped equally into high liver copper (HLC) and low liver copper (LLC) groups. Likewise, dataset 2 (a subset of dataset 1) containing 6 samples (HLC = 3; LLC = 3) was analyzed. The DEG analysis of HLC vs LLC groups for both data sets revealed a lower number of significant DEGs for dataset 1 (n = 64) when compared to dataset 2 (n = 252), respectively. Of the significant DEGs, 53 were jointly identified with both datasets. Identified DEGs downregulated in the HLC group including MVD, DHCR7, LOC101113583 and ERG28 are implicated in cholesterol synthesis, whereas AKR1B10 and CYP26A1 are associated with retinoic acid synthesis. The cholesterol biosynthetic process (GO:0006695) and the retinol metabolism (oas00830) were also observed by analysis of enriched gene ontologies, and Kyoto encyclopedia of genes and genomes pathways, respectively. Our findings provide new information on candidate genes associated with within-breed differences in hepatic copper concentration.