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

Abstract

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 sequencing (RNA-Seq) to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in 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 (false discovery ratio ≤0.001 and |log2 ratio| ≥1). Among the DGEs, we determined that 147 genes were downregulated and 85 genes were upregulated. Gene Ontology and KEGG Pathway analyses were performed to analyse 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. The results suggest that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our results provides unprecedented resolution of mRNAs that are expressed across the two breeds.