Transcriptome profiling of muscle by RNA-Seq reveals significant digital gene expression profiling differences between Angus and Luxi Cattle

The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA-Seq to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in both Chinese Luxi and Angus beef cattle. More than 9,243,921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (FDR=0.001 AND |log2Ratio|=1). Among the DGEs, we determined that 147 genes were down-regulated and 85 genes were up-regulated. GO and Pathway analysis were performed to analyze the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. This article suggests that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our result provides unprecedented resolution of mRNAs that are expressed across the two breeds. Overall design: Three Luxi and three Angus cattle that were eighteen months of age were generated by RNA-Seq