Simple SummaryThe eating experience of beef is strongly influenced by the amount of marbling or intramuscular fat. Beef steers are fed to a desired level of fatness in order to maximize the probability of a positive eating experience. This work aims to study the genes expressed in muscle and adipose tissue as beef steers deposit body fat to better understand the regulation of this important process and to more effectively predict positive eating experiences. This research identified genes that are altered as beef animals deposit fat in both the muscle and adipose tissues and the processes that are being altered, including the metabolism of fat and energy. The work also identified genes related to inflammation and injury in the adipose tissue that warrant additional research to further understand their role in beef animals.AbstractTargets for finished livestock are often determined by expected fat, either subcutaneous or intramuscular. These targets are used frequently to improve eating quality. Lower intramuscular fat, lack of product uniformity, and insufficient tenderness can negatively impact beef acceptability. This study aimed to investigate the differences in gene expression that alter metabolism and intercellular signaling in the muscle and adipose tissue in beef carcasses at different fat endpoints. In this study, longissimus thoracis muscle samples and adipose tissue were collected at harvest, and RNA was extracted and then sequenced using RNAseq. Differential expression was determined using edgeR, andp-values were adjusted using the Benjamini–Hochberg method. A correctedp-value of 0.005 and log2(fold change) of >1 were the threshold to identify differential expression. Comparison between intermuscular and subcutaneous fat showed no differences in the genes activated in the two adipose tissue depots, suggesting that subcutaneous fat was an adequate sample. Carcass data allowed the classification of carcasses by USDA quality grades (marbling targets). In comparing muscle from Standard and Choice carcasses, 15 genes were downregulated, and 20 were upregulated. There were 49 downregulated and 113 upregulated genes comparing adipose tissue from Standard and Choice carcasses. These genes are related to the metabolism of fat and energy. This indicates that muscle transcript expression varies less than adipose. In addition, subcutaneous fat can be used to evaluate transcript changes in fat. However, it is unclear whether these fat tissues can be used as surrogates for marbling.