Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency

Abstract

Identifying and breeding cattle that are more feed efficient is of great benefit to beef production. Additionally, it is crucial that genes contributing to feed efficiency are robust across varying management settings including dietary source as well as being relevant across contrasting breeds of cattle. The aim of this study was to determine miRNAs that are contributing to the expression of residual feed intake (RFI) across two breeds and dietary sources. miRNA profiling was undertaken in Longissimus dorsi tissue of Charolais and Holstein-Friesian steers divergent for RFI phenotype following two contrasting consecutive diets (high-forage and high-concentrate). Ten miRNA were identified as differentially expressed (adj. P < 0.1) across the breed and diet contrasts examined. Of particular interest was the differential expression of miR-2419-5p and miR-2415-3p, both of which were up-regulated in the Low-RFI Charolais steers across each dietary phase. Pathway analysis of target mRNA genes of differentially expressed miRNA revealed enrichment (P < 0.05) for pathways including metabolic related pathways, insulin receptor signalling, adipogenesis as well as pathways related to skeletal muscle growth. These results provide insight into the skeletal muscle miRNAome of beef cattle and their potential molecular regulatory mechanisms relating to feed efficiency in beef cattle.

Fig. 1

Overview of animal model.

Fig. 2

Venn diagram representing the differentially expressed miRNA between cattle divergent for RFI across varying breed type and offered contrasting dietary composition. CH-HF Charolais cattle under high-forage diet, HF-HF Holstein–Friesian cattle under high-froage diet, CH-HC Charolais cattle under high-concentrate diet, HF-HC Holstein–Friesian cattle under high-concentrate diet.

Fig. 3

AMPK signalling pathway enriched based on predicted target mRNA genes of miR-129-3p. Predicted target mRNA genes are highlighted in red and include CREB5 which displayed lower expression in the Holstein–Friesian steers following the HF diet (Keogh et al., 2023), whilst miR-129-3p followed the opposite direction of effect in the Holstein–Friesian steers at the same dietary phase, indicating a direct relationship between the miRNA and CREB5 gene.

Fig. 4

Adipogenesis pathway enriched based on predicted target mRNA genes of miR-7. Predicted target mRNA genes are highlighted in red and include FABP4 which displayed lower expressed in the CH steers following the HF diet (Keogh et al., 2023), whilst miR-7 followed the opposite direction of effect in the CH steers at the same dietary phase, indicating a direct relationship between the miRNA and FABP4 gene.