A Study of Applicability of SNP Chips Developed for Bovine and Ovine Species to Whole-Genome Analysis of Reindeer Rangifer tarandus

Veronika R Kharzinova; Alexander A Sermyagin; Elena A Gladyr; Innokentiy M Okhlopkov; Gottfried Brem; Natalia A Zinovieva

doi:10.1093/jhered/esv081

A Study of Applicability of SNP Chips Developed for Bovine and Ovine Species to Whole-Genome Analysis of Reindeer Rangifer tarandus

J Hered. 2015 Nov-Dec;106(6):758-61. doi: 10.1093/jhered/esv081. Epub 2015 Oct 7.

Authors

Veronika R Kharzinova¹, Alexander A Sermyagin², Elena A Gladyr², Innokentiy M Okhlopkov², Gottfried Brem², Natalia A Zinovieva²

Affiliations

¹ From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem). [email protected].
² From the L.K. Ernst Institute for Animal Husbandry, Dubrovitzy Estate, 60, Podolsk district, Moscow region, Podolsk 142132, Russia (Kharzinova, Sermyagin, Gladyr, Brem, and Zinovieva); Science Institute of Biological Problems Cryolithozone, Yakutsk 677980, Russia (Okhlopkov); and Institute for Animal Breeding and Genetics, VMU, A-1210 Vienna, Austria (Brem).

PMID: 26447215
DOI: 10.1093/jhered/esv081

Abstract

Two sets of commercially available single nucleotide polymorphisms (SNPs) developed for cattle (BovineSNP50 BeadChip) and sheep (OvineSNP50 BeadChip) have been trialed for whole-genome analysis of 4 female samples of Rangifer tarandus inhabiting Russia. We found out that 43.0% of bovine and 47.0% of Ovine SNPs could be genotyped, while only 5.3% and 2.03% of them were respectively polymorphic. The scored and the polymorphic SNPs were identified on each bovine and each ovine chromosome, but their distribution was not unique. The maximal value of runs of homozygosity (ROH) was 30.93Mb (for SNPs corresponding to bovine chromosome 8) and 80.32Mb (for SNPs corresponding to ovine chromosome 7). Thus, the SNP chips developed for bovine and ovine species can be used as a powerful tool for genome analysis in reindeer R. tarandus.

Keywords: SNP; reindeer Rangifer tarandus; whole-genome analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cattle
Genomics / methods*
Genotyping Techniques
Oligonucleotide Array Sequence Analysis*
Polymorphism, Single Nucleotide*
Reindeer / genetics*
Sheep
Species Specificity

Associated data

Dryad/10.5061/dryad.29FP0