Abstract
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.
Highlights
Single nucleotide polymorphisms (SNPs), the most common mutation in mammalian genomes, are single-base exchanges that naturally occur in the genome and have long been studied as valuable genetic markers, as they can affect and/or aid the selection of phenotypic traits [1,2]
SNP positioning of approximately ~56 million SNPs were acquired from the Run5 of the 1000 Bulls Genome Project (1000BGP; http://www.1000bullgenomes.com/) INDELS were not used in this study
Out of 193 miRNA mature sequences with SNPs, 91 had SNPs occurring within their seed region, and 70 of these 91 (77%) had changes in target prediction as a consequence of the nucleotide present
Summary
Single nucleotide polymorphisms (SNPs), the most common mutation in mammalian genomes, are single-base exchanges that naturally occur in the genome and have long been studied as valuable genetic markers, as they can affect and/or aid the selection of phenotypic traits [1,2]. Current genomic selection of production animals heavily relies on identification and genotyping of molecular markers such as SNPs [3]. Mutation mechanisms result in transitions when there are purine-purine or pyrimidine-pyrimidine exchanges and transversions in the case of purine-pyrimidine or pyrimidine-purine exchanges. SNPs affect miRNA target prediction in bovine
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