title: Catalog of genetic variants within mature microRNA seed regions in chicken.
abstract: MicroRNA (miRNA) is a class of noncoding RNA important in posttranscriptional regulation of target genes. The regulation mechanism requires complementarity between target mRNA and the miRNA region responsible for their recognition and binding, also called the seed region. It has been estimated that each miRNA targets approximately 200 genes and genetic variability of miRNA genes has been associated with phenotypic variation and disease susceptibility in humans, livestock species, and model organisms. Polymorphisms in miRNA genes especially within the seed region could therefore represent biomarkers for phenotypic traits important in livestock animals. Using the updated Version 5.0 of our previously developed bioinformatics tool miRNA SNiPer we assembled polymorphic miRNA genes in chicken. Out of 740 miRNA genes 263 were polymorphic, among them 77 had SNPs located within the mature region, and 29 of them within the miRNA seed region. Because several polymorphisms in databases result from sequencing errors, we performed experimental validation of polymorphisms located within 4 selected miRNA genes in chicken (gga-mir-1614, -1644, -1648, and -1657). We confirmed the presence of nine polymorphisms and identified 3 additional novel polymorphisms within primary miRNA regions in chicken representing 3 layer-type breeds, one layer-type hybrid, and one meat-type intercrossed population. The developed catalog of mir-SNPs in chicken can serve researchers as a starting point for association studies dealing with poultry production traits and designing functional experiments.
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia.
authors.forename: Minja
authors.initials: M
authors.lastname: Zorc
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia.
authors.forename: Sandra
authors.initials: S
authors.lastname: Omejec
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia.
authors.forename: Dusan
authors.initials: D
authors.lastname: Tercic
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia.
authors.forename: Antonija
authors.initials: A
authors.lastname: Holcman
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia.
authors.forename: Peter
authors.initials: P
authors.lastname: Dovc
authors.affiliation: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, SI-1230 Domzale, Slovenia tanja.kunej@bf.uni-lj.si.
authors.forename: Tanja
authors.initials: T
authors.lastname: Kunej
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D002645:Chickens / Q000235:genetics* / Q000378:metabolism; D003198:Computer Simulation; D005260:Female; D014644:Genetic Variation; D016678:Genome; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide
chemical_list: D030161:Avian Proteins; D035683:MicroRNAs
keywords: chicken; microRNA; seed region; single-nucleotide polymorphisms