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Background  In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important driver that affects IMF deposition.    Results  To reveal the intrinsic factors responsible for the low IMF content of buffalo, mRNA expression patterns in muscle and adipose tissue between buffalo and cattle were characterized by RNA sequencing analysis. The IMF content in Nanyang cattle was higher than that in Xinyang buffalo. A total of 1566 mRNAs expressed in adipose tissue showed differential expression between the  longissimus dorsi  muscles of buffalo and cattle. Functional annotation suggested a difference in the glycolysis/gluconeogenesis pathway between the two species. The results of RT-qPCR analysis and gain-of-function experiments confirmed the positive association between the IMF content and phosphoenolpyruvate carboxykinase 1 ( PCK1 ) expression in buffalo. In both mouse C2C12 cells and cultured bovine myocytes, the activity of the  PCK1  promoter in buffalo is lower than that in cattle. However, in mouse 3T3-L1 adipocytes and cultured bovine adipocytes, the activity of  PCK1  in buffalo promoter is higher than that in cattle.    Conclusions  These results indicate the important role of  PCK1  in buffalo IMF deposition and illustrate the differences between buffalo and cattle promoter activity that drive  PCK1  expression. This research helps to establish a foundation for further studies investigating IMF deposition in buffalo.

Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo