Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
Genet Sel Evol. 2021 May 4;53(1):43. doi: 10.1186/s12711-021-00632-3.
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.
成熟的 microRNAs（miRNAs）在抑制广泛的 mRNAs 表达方面发挥着重要作用。miRNA 基因及其相应的 3'UTR 结合位点中的多态性位点可能破坏规范的保守 miRNA-mRNA 配对，从而改变基因表达模式。然而，迄今为止，miRNA 基因中的多态性位点及其与基因表达表型和复杂性状的关联在猪中尚未得到很好的描述。
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，我们鉴定了 285 个映射到 miRNA 基因座的单核苷酸多态性（SNP），以及 109724 个位于猪 3'UTR 内预测的 7mer-m8 miRNA 结合位点的 SNP。在猪 miRNA 基因中，与侧翼非 miRNA 区域相比，SNP 密度降低。通过对五头杜洛克猪的基因组进行测序，我们鉴定了 12 个 miRNA SNPs，随后在其后代（Lipgen 群体，N=345）中进行了基因分型。对 miRNA SNPs 与 Lipgen 群体中记录的 38 个脂质相关性状和肝、肌肉微阵列表达表型之间的关联进行了分析。检测到的最相关关联是位于 ssc-miR-326 发夹前体顶端环的 rs319154814（G/A）SNP 的基因型与肝内 PPP1CC mRNA 水平之间的关联（q 值=0.058）。该结果随后通过 qPCR 得到了验证（P 值=0.027）。rs319154814（G/A）基因型也与几种脂肪酸组成性状有关。
我们的研究结果表明，猪 miRNA 基因的变异性降低，这与强烈的净化选择一致，特别是在 miRNA 结合中起关键作用的种子区域。尽管一般认为映射到种子区域的 SNP 是对 mRNA 表达影响最显著的 SNP，但我们表明，映射到 ssc-miR-326 顶端区域的 SNP 与 PPP1CC 基因的肝 mRNA 水平显著相关，该基因是其预测的靶点之一。虽然这种相互作用在人类中已有报道，但在猪中尚未报道，这一结果强调了需要进一步研究位于种子区域之外的 miRNA 多态性对猪基因表达的功能影响。
