Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil.
School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
PLoS One. 2021 Apr 21;16(4):e0249406. doi: 10.1371/journal.pone.0249406. eCollection 2021.
Single nucleotide polymorphisms (SNPs) can have significant effects on phenotypic characteristics in cattle. MicroRNAs (miRNAs) are small, non-coding RNAs that act as post-transcriptional regulators by binding them to target mRNAs. In the present study, we scanned ~56 million SNPs against 1,064 bovine miRNA sequences and analyzed, in silico, their possible effects on target binding prediction, primary miRNA formation, association with QTL regions and the evolutionary conservation for each SNP locus. Following target prediction, we show that 71.6% of miRNA predicted targets were altered as a consequence of SNPs located within the seed region of the mature miRNAs. Next, we identified variations in the Minimum Free Energy (MFE), which represents the capacity to alter molecule stability and, consequently, miRNA maturation. A total of 48.6% of the sequences analyzed showed values within those previously reported as sufficient to alter miRNA maturation. We have also found 131 SNPs in 46 miRNAs, with altered target prediction, occurring in QTL regions. Lastly, analysis of evolutionary conservation scores for each SNP locus suggested that they have a conserved biological function through the evolutionary process. Our results suggest that SNPs in microRNAs have the potential to affect bovine phenotypes and could be of great value for genetic improvement studies, as well as production.
单核苷酸多态性（SNPs）可以对牛的表型特征产生重大影响。微小 RNA（miRNAs）是一种小的非编码 RNA，通过与靶 mRNAs 结合，作为转录后调控因子发挥作用。在本研究中，我们对~5600 万个 SNPs 进行了扫描，针对 1064 个牛 miRNA 序列进行了分析，从理论上分析了它们对靶标结合预测、初级 miRNA 形成、与 QTL 区域的关联以及每个 SNP 位点的进化保守性的可能影响。在进行靶标预测后，我们发现 71.6%的 miRNA 预测靶标由于位于成熟 miRNA 种子区域内的 SNPs 而发生改变。接下来，我们确定了最小自由能（MFE）的变化，它代表了改变分子稳定性的能力，从而改变 miRNA 的成熟度。分析的序列中有 48.6%显示出了先前报道的足以改变 miRNA 成熟度的数值。我们还在 46 个 miRNA 中发现了 131 个 SNP，其靶标预测发生改变，出现在 QTL 区域。最后，对每个 SNP 位点的进化保守性评分进行分析表明，它们在进化过程中具有保守的生物学功能。我们的研究结果表明，miRNAs 中的 SNPs 有可能影响牛的表型，并且对遗传改良研究以及生产具有重要价值。
