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Background  This study used a genome-wide screen of gene expression to better understand the metabolic and functional differences between commercially valuable intramuscular fat (IMF) and commercially wasteful subcutaneous (SC) fat depots in  Bos taurus  beef cattle.    Results  We confirmed many findings previously made at the biochemical level and made new discoveries. The fundamental lipogenic machinery, such as  ACACA  and  FASN  encoding the rate limiting Acetyl CoA carboxylase and Fatty Acid synthase were expressed at 1.6–1.8 fold lower levels in IMF, consistent with previous findings. The FA elongation pathway including the rate limiting  ELOVL6  was also coordinately downregulated in IMF compared to SC as expected. A 2-fold lower expression in IMF of  ACSS2  encoding Acetyl Coenzyme A synthetase is consistent with utilisation of less acetate for lipogenesis in IMF compared to SC as previously determined using radioisotope incorporation. Reduced saturation of fat in the SC depot is reflected by 2.4 fold higher expression of the  SCD  gene encoding the Δ9 desaturase enzyme. Surprisingly,  CH25H  encoding the cholesterol 25 hydroxylase enzyme was ~ 36 fold upregulated in IMF compared to SC. Moreover, its expression in whole muscle tissue appears representative of the proportional representation of bovine marbling adipocytes. This suite of observations prompted quantification of a set of oxysterols (oxidised forms of cholesterol) in the plasma of 8 cattle exhibiting varying IMF. Using Liquid Chromatography-Mass Spectrometry (LC-MS) we found the levels of several oxysterols were significantly associated with multiple marbling measurements across the musculature, but (with just one exception) no other carcass phenotypes.    Conclusions  These data build on our molecular understanding of ruminant fat depot biology and suggest oxysterols represent a promising circulating biomarker for cattle marbling.

Gene expression identifies metabolic and functional differences between intramuscular and subcutaneous adipocytes in cattle