Comparing of backfat microRNAomes of Landrace and Neijiang pig by high-throughput sequencing

Abstract

MicroRNAs (miRNAs) could regulate the expression of target genes and play important roles in modulation of various metabolic processes. Nevertheless, little is known about the backfat microRNAome (miRNAome) of the Neijiang pig. The primary objective of this study was to analyse miRNAomes of Landrace and Neijiang pig backfat (LPB and NPB resp.). Furthermore, investigating differentially expressed miRNAs participating in lipid metabolism and mining potential biomarker for Neijiang pig breeding. Here we used the Landrace pig with different metabolic characteristics as a control to analyse the Neijiang pig-specific backfat miRNAome. A comprehensive analysis of miRNAomes was performed by deep sequencing. Small RNA sequencing identified 326 unique miRNAs, 280 were co-expressed in both libraries. Only 11 and 35 miRNAs were specifically expressed in LPB and NPB respectively. Sixty seven differentially expressed miRNAs were identified by IDEG6. MiR-1-3p were identified that may participate in lipid metabolism. Furthermore, qPCR results revealed that lower expression of miR-1-3p in NPB could increase the expression of LXRα, which is an enzyme important for the synthesis and accumulation of lipid. The double luciferase report experiment suggested that LXRα was the direct target gene of miR-1-3p. In short, miR-1-3p could modulate the synthesis and accumulation of lipid by target LXRα. It may be a potential marker for pig breeding. Our investigation has delineated the different miRNAs expression patterns of LPB and NPB, which may help understand the regulatory mechanisms of miRNAs in the lipid metabolism, and provide potential biomarkers for Neijiang pig breeding.