Single nucleotide polymorphisms affect miRNA target prediction in bovine

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.

Association between novel variants in BMPR1B gene and litter size in Mongolia and Ujimqin sheep breeds

“…Duan et al (2003) reported that some synonymous mutations led to a decrease in mRNA stability and translation, and dramatically changed dopamine-induced upregulation of DRD2 expression. In addition, a study observed that the presence of SNPs can alter hairpin conformation due to loss or acquisition of base pairing, consequently altering free energy in primary miRNAs (Sousa et al, 2021). Also, the c.1470G>T mutation is predicted to change the mRNA secondary structure of BMPR1B.…”

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

“…Water buffalo miRNAs and SNPs can be further used as genomic resources. Such use has been reported in cattle where SNPs and miRNAs have been found associated with bovine phenotypes to be used in breed improvement ( Sousa et al, 2021 ).…”

First DNA Sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants

“…Furthermore, two SNP in the 3 -UTR induce the deletion and/or the substitution of several miRNA binding sites. Some of these miRNA were associated with milk production traits including milk fat metabolism [72,73]. Therefore, the impact of the alteration/substitution of miRNA target sites from SNP in 3 -UTR of CSN1S2 would be interesting for investigations in an experimental study.…”