Genome‐wide in silico screening for microRNA genetic variability in livestock species

Abstract

MicroRNAs are a class of non-coding RNAs that post-transcriptionally regulate target gene expression. Previous studies have shown that microRNA gene variability can interfere with its function, resulting in phenotypic variation. Polymorphisms within microRNA genes present a source of novel biomarkers for phenotypic traits in animal breeding. However, little is known about microRNA genetic variability in livestock species, which is also due to incomplete data in genomic resource databases. Therefore, the aim of this study was to perform a genome-wide in silico screening of genomic sources and determine the genetic variability of microRNA genes in livestock species using mirna sniper 3.0 (http://www.integratomics-time.com/miRNA-SNiPer/), a new version of our previously developed tool. By examining Ensembl and miRBase genome builds, it was possible to design a tool-based generated search of 16 genomes including four livestock species: pig, horse, cattle and chicken. The analysis revealed 65 polymorphisms located within mature microRNA regions in these four species, including 28% within the seed region in cattle and chicken. Polymorphic microRNA genes in cattle and chicken were further examined for mapping to quantitative trait loci regions associated with production and health traits. The developed bioinformatics tool enables the analysis of polymorphic microRNA genes and prioritization of potential regulatory polymorphisms and therefore contributes to the development of microRNA-based biomarkers in livestock species. The assembled catalog and the developed tool can serve the animal science community to efficiently select microRNA SNPs for further quantitative and molecular genetic evaluations of their phenotypic effects and causal associations with livestock production traits.

Effect of pre-miRNA-1658 gene polymorphism on chicken growth and carcass traits

“…Zorc et al [35] found that some miRNAs had highly polymorphic seed regions, pre-miRNA gga-mir-1658 had one SNP within the mature sequence ( gga-miR-1658 ) and two SNPs within the minor miR sequence ( gga-miR-1658 *), in addition, in chicken gga-miR-1658 with seven quantitative trait locus. Jevsinek et al [36] reported that polymorphisms residing within the miRNA seed region of chicken gga-mir-1658 were selected for experimental validation. The rs16681031 and rs16681032 SNP is located in seed regions of chicken gga-mir-1658-3p which resides in the intron 13 of miRNA host guanine monphosphate synthetase ( GMPS ) gene, the rs16681033 SNP is located in seed regions of gga-mir-1658-5p which resides in the intron 13 of GMPS gene [36].…”

“…Jevsinek et al [36] reported that polymorphisms residing within the miRNA seed region of chicken gga-mir-1658 were selected for experimental validation. The rs16681031 and rs16681032 SNP is located in seed regions of chicken gga-mir-1658-3p which resides in the intron 13 of miRNA host guanine monphosphate synthetase ( GMPS ) gene, the rs16681033 SNP is located in seed regions of gga-mir-1658-5p which resides in the intron 13 of GMPS gene [36]. Geng et al [37] reported that the rs16681031 SNP located in seed regions of gga-mir-1658 * in 6 chicken populations 180 individuals.…”

Genome-Wide Association Study Identifies Phospholipase C zeta 1 (PLCz1) as a Stallion Fertility Locus in Hanoverian Warmblood Horses

“…The pattern of miRNAs expressed in infertile men suggested their role in regulating male germ and somatic cells and that their alteration is associated with reproductive abnormalities [65] . A recent study in livestock animals including horses showed a profound effect of miRNA polymorphisms on a wide range of phenotypic traits in animal production [66] . The miRNA motif when removed by the SNP g.45599001G>A may alter protein expression level of PLCz1.…”

Genetic variants in microRNA biogenesis genes as novel indicators for secondary growth in Populus

“…Additionally, allelic SNPs occur widely within miRNA genomic regions, including the flanking regions and pre‐mature regions (Gong et al ., ; Jevsinek Skok et al ., ; Liu et al ., ). The binding sites and flanking regions of target genes of specific miRNAs also harbored abundant mutations (Liu et al ., ; Hogg & Harries, ).…”