Mitochondria are primarily organelles for cellular energy metabolism andhave a maternally inherited genome encoding 37 genes. Proteins fromthese genes interact with mitochondrial proteins (MP) encoded by nucleargenes to enable mitochondrial functions. Given the key role of mitochondriain energy production, mutations affecting the expression of MP genescould have flow-on effects on important traits in cattle. Our study had 3aims: first to assess the diversity of the mitochondrial genome of moderndairy cattle breeds, second, to characterize MP gene expression acrosstissues within animals, and third, to correlate MP gene expression in bloodwith feed efficiency in dairy cattle. Mitochondrial genome diversities (nucleotideand haplotype) were estimated based on selected variant positionsacross the genome. Overall, there was a low diversity in the dairy breedsstudied. Broadly, the modern dairy cattle (e.g., Holsteins) were predominantlyT3 (~95%, with > 10 evident subgroups) and to a lesser extent T2and T1 haplogroups. Gene expression in tissue as was quantified by RNAsequencing. We used differential expression and co-expression analysesof genes in 29 tissues from 2 cows. We found consistent overexpression inhigh energy demand tissues (e.g., heart). This suggests that MP gene expressionmight also differ between animals that differ within tissue energydemands. We, therefore, measured gene expression in blood samples of 2groups (14 dairy cows each) divergent for feed efficiency to analyze thedifferential gene expression and co-expression networks. There were 395genes differentially expressed (DE) between high and low feed efficiencygroups, of which 55 were MP genes. Furthermore, DE genes were significantlyenriched for oxidative phosphorylation (OxPhos), an importantpathway that generates cellular energy. However, none of the DE MP geneswas from the mitochondrial genome. The association between feed efficiencyand expression of MP genes involved in the OxPhos pathway wasalso evident in a weighted gene co-expression network analysis (r = 0.47,P = 0.01). Altogether, our study suggests that there is low mitochondrialgenomic diversity among popular dairy breeds and MP gene expressionmay be associated with variation in traits linked to mitochondrial function.
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