Genomic and transcriptomic analyses for markers, genes and regions associated with liver copper concentration in sheep

Abstract

The continuous economic and health impact of copper (Cu) intoxication and deficiency in sheep farming necessitates the need to understand the influence of the ovine genome on within- and between-breed differences in liver Cu concentration in sheep. In our studies, within-breed variations in liver Cu concentration observed in flocks under similar dietary and environmental conditions ranged from 30% to 55%. The heritability estimate and accuracy (0.67 ± 0.29) observed in our study was similar to values of 0.60± 0.32 found in previous studies. Therefore, it can be concluded that this trait is most likely heritable, and it is influenced by genetic factors. To this end, we tested the probability that certain SNP markers of the ovine genome may be associated with variability in liver Cu concentration in sheep using single- and multi-locus GWAS methods. The results revealed that a total of 13 markers, identified using ML-GWAS, were associated with variability in liver Cu concentration in Merinoland sheep. Functional enrichment analysis revealed enriched GO terms such as lysosomal membrane and mitochondrial inner membrane. To support this finding, a comparative transcriptome analysis between liver samples of Polish Merino sheep with low and high hepatic Cu concentration was performed. Among the differentially expressed genes was the SPATC1L gene, which is located 148.7 Kb from a SNP (rs427314005) identified by GWAS before. Enriched GO and KEGG pathway terms including cholesterol and retinoic acid syntheses were identified. Furthermore, we performed selection signature analysis to identify genomic regions under selection between Cu-susceptible and Cu-tolerant sheep breeds. Findings from this study showed that regions on OAR 4, 8 and 11 are under selection for this trait. In addition, lipoxygenase and ferroptosis pathways were identified among others as enriched GO and KEGG pathway terms. The results of the present work point to a polygenic nature of within- and between-sheep breed differences in liver Cu concentration. Additionally, our different studies suggest that pathways responsible for within-breed variation of liver Cu concentration sheep differ from those affecting between-breed variation of this trait. Further studies need to be conducted to confirm identified regions, genes or markers associated with variability in liver Cu concentration and their potential use in animal breeding.