Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content

The pig provides meat products for human consumption on a large scale. High-throughput sequencing technology provides a powerful approach for the characterization of the muscle transcriptome of pigs. Despite many studies using high-throughput technologies, the functional complexity of porcine muscle transcriptome is not fully elucidated. Therefore, the aim of this study was to gain insight into the longissimus lumborum muscle transcriptome between two pig breeds with distinct phenotypes, Laiwu pig, a Chinese indigenous pig breed, and Yorkshire pig, a Western breed. RNA-seq was applied to sample transcripts of the longissimus lumborum muscle between the two pig breeds to gain insights into whole-genome transcription profiles. For the Laiwu and Yorkshire libraries, we obtained a total of 40,498,476 and 59,072,892 high quality reads, respectively. Moreover, the resulting data set provided expression patterns for many annotated, predicted and novel pig genes. 178 significantly differentially expressed genes were identified between the Laiwu and Yorkshire pigs, with 98 up-regulated and 80 down-regulated genes in Laiwu pig compared with Yorkshire pig. Gene expression results of the RNA-seq data were validated by qRT-PCR for twelve genes. Genes that were differentially expressed were involved in lipid metabolism and were more highly expressed in Laiwu pigs. The present study provides a comprehensive view of differences in the muscle transcriptome between two pig phenotypes. These results expand our knowledge of the genes transcribed in the skeletal muscle of two breeds and provide a basis for future research of the molecular mechanisms underlying the phenotypic differences on meat quality.