Characterization and differential expression of microRNA in skeletal muscle of Laiwu and Yorkshire pig breeds

The domestic pig is an important agricultural animal used as a source of meat worldwide. As an important resource, Laiwu pig has some special characteristics compared with Yorkshire pig. It is necessary to identify the differentially expressed microRNAs (miRNAs) in skeletal muscle between two pig breeds. Therefore, we herein performed a comprehensive investigation for miRNA transcriptome of skeletal muscle from the two pig breeds. On average, we obtained approximately 13,493,607 clean reads in Laiwu pig and 12,938,257 clean reads in Yorkshire pig in this study. Totally, 265 known miRNAs were identified, and among these, 229 miRNAs were expressed in all the six pigs. From the 265 known miRNAs, 19 of these miRNAs were found significantly differentially expressed (q < 0.05). Of these significantly expressed miRNAs, seven miRNAs were significantly up-regulated and 12 miRNAs were down-regulated in Laiwu pig compared with Yorkshire pig. Among the significantly expressed miRNAs, ssc-miR-194-5p has the largest fold-change (6.35-fold). Ten differentially expressed miRNAs selected from high throughput sequencing were confirmed by real-time RT-PCR (RT-qPCR), and the results indicated that the expression patterns were consistent with sequencing results. Our results not only present a comprehensive miRNA transcriptome profile of skeletal muscle between two pig breeds with distinct phenotypes, but also could be useful for investigating the functions of differentially expressed miRNAs associated with the phenotype traits.