Sel’skokhozyaistvennaya Biologiya [Agricultural Biology], 2017, V. 52, № 4, pp. 669-678
(how to cite this article)

doi: 10.15389/agrobiology.2017.4.669eng

UDC 636.294:575.174.015.3

Acknowledgements:
Equipment of the Collective Center Agricultural Animals’ Bioresources and Bioengineering of the L.K. Ernst Federal Science Center for Animal Husbandry was used in the study Supported financially by Russian Science Foundation (project No. 14-36-00039)

 

POPULATION-GENETIC CHARACTERISTICS OF DOMESTIC
REINDEER OF YAKUTIA BASED ON WHOLE-GENOME SNP
ANALYSIS

V.R. Kharzinova1, A.V. Dotsev1, A.D. Solovieva1, V.I. Fedorov2,
I.M. Okhlopkov3, K. Wimmers4, H. Reyer4, G. Brem1, 5,
N.A. Zinovieva1

1L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, 60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia,
e-mail veronika0784@mail.ru (corresponding author), asnd@mail.ru, anastastasiya93@mail.ru, n_zinovieva@mail.ru;
2M.G. Sofronov Yakutsk Research Institute of Agriculture,Federal Agency of Scientific Organizations, 23/1, ul. Bestuzheva-Marlinskogo, Yakutsk, Sakha Republic (Yakutia), 677001 Russia, e-mail vfedorov_09@mail.ru;
3Institute for Biological Problems of Cryolithozone Siberian Branch of RAS, Federal Agency of Scientific Organizations, 41, pr. Lenina, Yakutsk, Sakha Republic (Yakutia), 677000 Russia, e-mail imo-ibpc@yandex.ru;
4Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Mecklenburg-Vorpommern, 18196 Dummerstorf, Germany,
e-mail wimmers@fbn-dummerstorf.de, reyer@fbn-dummerstorf.de;
5Institut für Tierzucht und Genetik, University of Veterinary Medicine (VMU), Veterinärplatz, A-1210, Vienna, Austria, e-mail gottfried.brem@vetmeduni.ac.at

The authors declare no conflict of interests

ORCID:

Kharzinova V.R.
orcid.org/0000-0002-8067-0404

Wimmers K.
orcid.org/0000-0002-9523-6790

Dotsev A.V.
orcid.org/0000-0003-3418-2511

Reyer H.
orcid.org/0000-0001-6470-0434

Solovieva A.D.
orcid.org/0000-0003-2628-9554

Brem G.
orcid.org/0000-0002-7522-0708

Fedorov V.I.
orcid.org/0000-0002-8454-6531

Zinovieva N.A.
orcid.org/0000-0003-4017-6863

Okhlopkov I.M.
orcid.org/0000-0002-6227-5216

 

Received May 23, 2017

 

The Republic of Sakha (Yakutia) is one of the main reindeer herding regions of the Russian Federation. The census population size of domesticated reindeer in the Sakha Republic amounts to more than 156 thousand individuals. Three of the four officially recognized breeds are being bred in Yakutia: the Even, Evenk and Chukotka (Khargin). The analysis of single nucleotide polymorphisms (SNPs) using DNA microarrays (DNA chips) is the useful tool to assess and preserve the biodiversity of this important agricultural species. In the present work, we have used the Bovine SNP50 BeadChip to determine the genotypes and population-genetic characteristics of three domestic reindeer originated from the territory of the Republic of Sakha (Yakutia). Tissue samples (ear skin samples) from reindeer of the breeds Even (EVN, n = 8), Evenk (EVK, n = 11) and Chukotka (CHU, n = 7) were used as biological material for the study. The PLINK 1.07 software was used to check the quality of genotyping. For data processing, we used the software PLINK 1.07, Admixture 1.3, and R packages diveRsity, VennDiagram with subsequent visualization in the R packages pophelper and ggplot2. According to the results of quality control, we selected 512 polymorphic SNPs for further analysis. Analysis of Venn-diagrams showed that the reindeer of Even and Evenk breeds have a maximal number of unique polymorphisms (14 SNPs). Eleven unique SNPs were detected in the Chukotka breed. The calculation of basic population parameters revealed that individuals of the Chukotka breed are characterized by higher levels of genetic diversity (Ho = 0.180±0.011, He = 0.156±0.008, Ar = 1.488±0.022) and a higher excess of heterozygotes (FIS = -0,124), compared to Evenk (Ho = 0.161±0.009, He = 0.153±0.008, Ar = 1.487±0.020, and FIS = -0,047) and Even (Ho = 0.164±0.010, He = 0.149±0.008, Ar = 1.471±0.021, and FIS = -0.089) breeds. The results of multidimensional scaling and the calculation of pairwise genetic distances (FST) showed the greatest closeness of the breeds Even and Evenk. Admixture analysis revealed a high degree of genetic isolation of each of the studied breeds. However, among the domestic reindeer of Chukotka and Evenk breeds we identified individuals with a mixed genetic origin, which is close to Even genetics. The obtained data will be applied in the development of programs for the conservation and sustainable use of this important animal species.

Keywords: single nucleotide polymorphism, genetic diversity, reindeer breeds.

 

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