Inactivity-related diseases (such as obesity and insulin resistance) are a burden on Western society, with low cardiorespiratory fitness (maximal aerobic capacity, VO2max) a strong independent predictor of metabolic disease and all-cause mortality. The etiological basis of these disorders is polygenic and highly dependent on the environment (i.e., existing genes interact with environmental factors to result in phenotypic expression of these diseases). The work undertaken for this thesis comprised a series of independent but related studies aimed at enhancing our understanding of the relationship between genetic factors and environmental stimuli in determining the capacity for aerobic energy production in skeletal muscle and white adipose tissue (WAT). Rodent models of divergent intrinsic running capacity (and, by association, metabolic health profile) and environmental interventions (i.e., diet and exercise) were employed in order to explore some of the mechanisms that determine the capacity for mitochondrial energy production in these two insulin-responsive tissues. In the first investigation (Chapter 2), Long-Evans rats were given ad libitum access to either a Western Diet (WD; 40% energy (E) from fat, 17 % protein, and 43% carbohydrate (30% sucrose); n=12) or a control diet (CON; 16% E from fat, 21% protein, and 63% carbohydrate (10% sucrose); n=12) for 12 wk. Rats fed the WD consumed 23% more E than CON (P=0.0001), which was associated with greater increases in body mass (23%; P=0.0002) and adiposity (17%; P=0.03). There were no differences in fasting blood glucose concentration of glucose tolerance between diets, although fasting insulin was increased by 30% (P=0.007). Fasting serum triglycerides were also elevated in WD (86%; P=0.001). The maximal respiratory capacity of m. soleus (soleus) was greater following the WD (37%; P=0.02), as were the maximal activities of several mitochondrial enzymes (citrate synthase, CS; β-hydroxyacyl-CoA dehydrogenase, β-HAD; carnitine palmitoyltransferase). Protein expression of CS, uncoupling protein (UCP)-3, and individual respiratory complexes was greater after WD (all P<0.05) despite no differences in the expression of peroxisome proliferator activated receptor-γ coactivator-1α (PGC-1α) mRNA or protein. The finding that the mitochondrial machinery was increased in skeletal muscle in response to the WD led to the conclusion that mitochondrial energy production pathways were up-regulated in order to cope with the sudden increased flux of energy substrates to metabolically active tissues. It was suggested that elevated skeletal muscle respiratory capacity would be, at least in the short term, protective against lipid-induced impairments in glycemic control. Given that VO2max also has a genetic underpinning, the second investigation (Chapter 3) sought to identify whether intrinsic running capacity (and, by association, metabolic health) was associated with skeletal muscle mitochondrial content and/or oxidative capacity. Eleven-wk old genetically heterogeneous rats with inborn high- (HCR) and low- (LCR) running capacity were studied in the absence of exercise training. LCR rats (n=12) were 28% heavier (P=0.0001), and fasting serum insulin concentrations were 62% greater than in HCR rats (n=12; P=0.02). In contrast, HCR rats had better glucose tolerance (P=0.01) and reduced adiposity (P=0.02). In soleus, maximal respiratory capacity was 21% greater in HCR rats (P=0.001), for which the relative contribution of fat oxidation was 20% higher than LCR rats (P=0.02). This was associated with increased CS (33%; P=0.009) and β-HAD activities (33%; P=0.0003). In m. extensor digitorum longus (EDL), CS activity was 29% greater (P=0.01) and β-HAD activity was 41% greater (P=0.0004) in HCR compared to LCR rats. Mitochondrial DNA was also elevated in the EDL of HCR rats (35%; P=0.049) and soleus (44%; P=0.16). Additionally, HCR rats had increased protein abundance of individual mitochondrial respiratory complexes, CS, and UCP-3 in both muscle types (all P<0.05). The finding that both mitochondrial machinery and capacity were elevated in HCR compared to LCR rats is consistent with the observation that endurance trained individuals have a greater reliance on lipid-based fuels as an energy source, and explains, in part, how intrinsically determined skeletal muscle metabolism contributes to the phenotype of running capacity and its correlated traits. WAT plays a central role in regulating whole-body lipid metabolism, with the metabolic activity of WAT being a crucial factor for substrate metabolism in other peripheral tissues. Thus, the primary aim of the third investigation (Chapter 4) was to characterize the expression and activity of mitochondrial proteins important to energy production pathways in WAT from the LCR and HCR rat phenotypes. Additionally, since exercise training has recently been shown to alter important aspects of WAT energy metabolism (such as improved insulin action and elevated expression of PGC- 1α and UCP-1), the effect of a short-term treadmill running protocol (same cumulative distance (~10 km) over 6 wk) on WAT from LCR and HCR rats was also investigated. LCR and HCR rats (n=10 per group, 22 wk old) were studied with or without exercise training. In untrained rats, the abundance of individual mitochondrial respiratory complexes, CS, and PGC-1α was similar for both phenotypes, although, CS activity showed a tendency to be greater in HCR (50%; P=0.09). Exercise training increased CS activity in both phenotypes but did not alter mitochondrial protein content. Training increased the expression and phosphorylation of proteins with roles in β-adrenergic signaling, including the β3-adrenergic receptor (increased 16% in LCR; P<0.05), neuron-derived orphan receptor-1 (decreased 24% in LCR and 21% in HCR; both P<0.05), phosphor-adipose triglyceride lipase (increased 25% in HCR; P<0.05), perilipin (increased 25% in HCR; P<0.05), comparative gene identification-58 (increased 15% in LCR; P<0.05), and the glucose transport protein GLUT4 (increased 16% in HCR; P<0.0001). A training effect was also observed for the phosphorylation status of the stress kinases p38 mitogen-activated protein kinase (decreased 12% in LCR and 20% in HCR; both P<0.05) and c-JuN terminal kinase 1/2 (increased 29% in LCR and 20% in HCR; both P<0.05). It was concluded that in the LCR-HCR rat model system, mitochondrial protein expression in WAT is not affected by intrinsic running capacity or short-term exercise training. However, training does induce alterations in the activity and expression of several proteins that are essential to the intracellular regulation of WAT metabolism. In summary, this thesis has identified several novel mechanisms by which mitochondrial function/adaptations can influence the capacity for energy substrate metabolism in skeletal muscle and WAT