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 polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 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 flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (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 confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. Our findings 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 generally 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 significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.

中文翻译：

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猪微小RNA基因的变异性及其与mRNA表达和脂质表型的关系

成熟的 microRNA (miRNA) 在抑制多种 mRNA 的表达方面发挥着重要作用。miRNA 基因中多态位点的存在及其相应的 3'UTR 结合位点可以破坏经典保守的 miRNA-mRNA 配对，从而改变基因表达模式。然而，迄今为止，miRNA 基因中的此类多态位点及其与基因表达表型和复杂性状的关联在猪中的特征还很差。通过分析来自欧洲和亚洲的 120 头猪和野猪的全基因组序列，我们确定了 285 个定位到 miRNA 基因座的单核苷酸多态性 (SNP)，以及位于猪 3' 内预测的 7mer-m8 miRNA 结合位点的 109,724 个 SNP UTR。在猪 miRNA 基因中，与其侧翼的非 miRNA 区域相比，SNP 密度降低。通过对五头杜洛克公猪的基因组进行测序，我们鉴定了 12 个 miRNA SNP，这些 SNP 随后在其后代中进行了基因分型（N = 345，Lipgen 种群）。进行了 miRNA SNP 与 38 个脂质相关性状以及在 Lipgen 群体中记录的肝脏和肌肉微阵列表达表型的关联分析。检测到的最相关的关联是位于 ssc-miR-326 发夹前体顶端环的 rs319154814 (G/A) SNP 的基因型与肝脏中的 PPP1CC mRNA 水平（q 值 = 0.058）。这一结果随后被 qPCR 证实（P 值 = 0.027）。rs319154814 (G/A) 基因型也与几种脂肪酸组成特征相关。我们的研究结果表明猪 miRNA 基因的变异性降低，这与强纯化选择一致，特别是在 miRNA 结合中起关键作用的种子区域。尽管通常假设映射到种子区域的 SNP 对 mRNA 表达的影响最显着，但我们表明映射到 ssc-miR-326 顶端区域的 SNP 与 PPP1CC 基因的肝脏 mRNA 水平显着相关，其预测目标之一。尽管在人类中报道了这种相互作用的实验证实，但在猪中没有报道，但该结果强调需要进一步研究位于种子区域外的 miRNA 多态性对猪基因表达的功能影响。其预测目标之一。尽管在人类中报道了这种相互作用的实验证实，但在猪中没有报道，但该结果强调需要进一步研究位于种子区域外的 miRNA 多态性对猪基因表达的功能影响。其预测目标之一。尽管在人类中报道了这种相互作用的实验证实，但在猪中没有报道，但该结果强调需要进一步研究位于种子区域外的 miRNA 多态性对猪基因表达的功能影响。