Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

Abstract

Background: Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3′UTR binding sites can disrupt canonical conserved miRNA–mRNA pairings, and thus modify gene expression patterns. However, to date such poly‑ morphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. Results: By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identifed 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3′UTR. In porcine miRNA genes, SNP density is reduced compared with their fanking non-miRNA regions. By sequencing the genomes of fve Duroc boars, we identifed 12 miRNA SNPs that were subsequently genotyped in their ofspring (N=345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value=0.058). This result was subsequently confrmed by qPCR (P-value=0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. Conclusions: Our fndings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is gener‑ ally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is signifcantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confrmation of such an interac‑ tion is reported in humans but not in pigs, this result highlights the need to further investigate the functional efects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.