Targets 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, and p-values were adjusted using the Benjamini–Hochberg method. A corrected p-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.

Targets for finished livestock are often determined by expected fat, either subcutaneous or intramuscular. These targets are used frequently to improve the chances of acceptable eating quality. Lower intramuscular fat, lack of product uniformity, and reduced or insufficient tenderness can negatively impact beef acceptability. This study aimed to investigate differences in gene expression that potentially alter subsequent metabolism and intercellular signaling in the muscle and proximate intermuscular and subcutaneous adipose tissue in beef carcasses at different fat endpoints. In this study, Longissimus thoracis muscle samples and associated adipose tissue were collected at harvest. RNA was harvested from both tissues, and individual samples were sequenced using RNAseq. Differential expression was determined using edgeR, and p-values were adjusted using the Benjamini-Hochberg method. A corrected p-value of 0.005 and log₂ (fold change) of 1 was set as the threshold to identify differential expression of genes. Comparison between intermuscular fat and subcutaneous fat showed no differences between the genes activated in the two adipose tissue depots, suggesting that subcutaneous fat could be sampled to evaluate changes in adipose tissue. Carcass data allowed the classification of carcasses by projected USDA quality grades (marbling targets). In the comparison between muscle from Standard and Choice carcasses, 15 genes were downregulated, and 20 were upregulated. The insulin receptor substrate 1 (IRS 1) gene was the only known functionally important gene to be differentially expressed. There were 49 downregulated genes and 113 upregulated genes in the comparison between adipose tissue from Standard and Choice carcasses. These genes are mostly related to the metabolism of fat and energy. This potentially indicates that muscle is not changing at the transcript level as much as the adipose tissue at the sampled endpoints. Also, subcutaneous fat can be used to evaluate transcript changes in both subcutaneous and intermuscular fat. However, it is not clear if these fat tissues can be used as surrogates for intramuscular fat or marbling.