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Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2019, Vol. 54, № 6, p. 1167-1176.
(how to cite this article)

doi: 10.15389/agrobiology.2019.6.1167eng

UDC: 636.294:575.174:575.113:577.2.08

Acknowledgements:
The equipment of the Sharing Center for Farm Animal Bioresources and Bioengineering (FSC for Animal Husbandry) was used.
Supported financially by Russian Science Foundation, project 16-16-10068-P

 

DEVELOPMENT AND VALIDATION OF A LOW DENSITY SNP PANEL FOR ASSESSMENT OF GENETIC DIVERSITY OF THE REINDEER (Rangifer tarandus) POPULATIONS

V.R. Kharzinova1, T.E. Deniskova1, A.V. Dotsev1, A.D. Solovieva1,
T.M. Romanenko2, K.A. Laishev3, V.I. Fedorov4, I.M. Okhlopkov5,
H. Reyer6, K. Wimmers6, G. Brem1, 7, N.A. Zinovieva1

1Ernst Federal Science Center for Animal Husbandry, 60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia, e-mail horarka@yandex.ru (✉ corresponding author),veronika0784@mail.ru, asnd@mail.ru, anastastasiya93@mail.ru, n_zinovieva@mail.ru;
2Laverov Federal Center for Integrated Arctic Research (FCIARctic) RAS, Naryan-Mar Agro-Experimental Station, 1a, ul. Rybnikov, Naryan-Mar, Nenets AO, 166004 Russia, e-mail nmshos@atnet.ru;
3Northwest Center for Interdisciplinary Research of Food Security Problems, 7, sh. Podbel’skogo, St. Petersburg—Pushkin, 196608 Russia, e-mail layshev@mail.ru;
4Safronov Yakutsk Research Institute of Agriculture, Siberian Branch RAS, 23/1, ul. Bestuzheva-Marlinskogo, Yakutsk, Sakha Republic, 677001 Russia, e-mail vfedorov_09@mail.ru;
5Institute for Biological Problems of Cryolithozone, Siberian Branch RAS, 41, prosp. Lenina, Yakutsk, Sakha Republic, 677980 Russia, e-mail imo-ibpc@yandex.ru;
6Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Mecklenburg-Vorpommern, 18196 Dummerstorf, Germany, e-mai reyer@fbn-dummerstorf.de, wimmers@fbn-dummerstorf.de;
7Institut für Tierzucht und Genetik, University of Veterinary Medicine (VMU), Veterinärplatz, A-1210, Vienna, Austria, e-mail gottfried.brem@agrobiogen.de

ORCID:
Kharzinova V.R. orcid.org/0000-0002-8067-0404
Fedorov V.I. orcid.org/0000-0002-8454-6531
Deniskova T.E. orcid.org/0000-0002-5809-1262
Okhloplov I.M. orcid.org/0000-0002-6227-5216
Dotsev A.V. orcid.org/0000-0003-3418-2511
Reyer H. orcid.org/0000-0001-6470-0434
Solovieva А.D. orcid.org/0000-0002-1437-2521
Wimmers K. orcid.org/0000-0002-9523-6790
Romanenko Т.М. orcid.org/0000-0002-5572-5995
Brem G. orcid.org/0000-0002-7522-0708
Layshev К.А. orcid.org/0000-0003-2490-6942
Zinovieva N.A. orcid.org/0000-0003-4017-6863

Received August 6, 2019

 

Reindeer (Rangifer tarandus) is a valuable member of the Arctic ecosystems and the main livestock species of the Russian North, which require the analysis of the genetic structure and the possibility of addressing the differences between wild and domestic forms, breeds and populations using modern molecular genetic approaches. The use of DNA chips based on parallel genotyping of hundreds of thousands of SNP markers is an effective approach to study the reindeer genome, but at the same time due to a high price, it is not beneficial for wide practical application. In this regard, the aim of our work is to select the optimal number of SNP markers that allow conducting population and genetic studies of reindeer without loss of bio-informatics content. The sample collection included wild deer (WLD, n = 83) inhabiting the Taimyr Peninsula and the Republic of Sakha (Yakutia), and domestic deer of the Nenets breed from the Nenets Autonomous Okrug (NEN, n = 100) and the Murmansk Region (MUR, n = 19), as well as from Even and Evenki breeds from the Republic of Sakha (Yakutia) (YAK, n = 19). All deer were genotyped using a high-density DNA chip BovineHD BeadChip (777,962 SNPs). After quality control and filtering, 4456 polymorphic SNP markers remained in the analysis. In the TRES program, using the Delta method, 368 of the most informative SNP markers were selected. Data processing was performed in the Admixture 1.3, PLINK 1.9 programs and R packages (ggplot2, adegenet 1.3-1, pophelper, diveRsity). It was shown that 70 % from 368 selected SNPs had a high minor allele frequency (MAF ≥ 0.3), while about 50 % from set including 4456 markers had MAF ≤ 0.1. Comparing the results of principal component analysis (PCA), discriminant principal component analysis (DAPC), and cluster analysis, no loss of information value was found for 368 SNPs compared to using the set of 4456 markers. Comparing pairwise FST values between the studied groups of reindeer, the similarity of the interpopulation linkages was demonstrated, based on 4456 and 368 SNP markers, respectively. Thus, the selected panel of SNP markers is an informative, universal for both wild and domestic deer and a cheap approach for creating a custom DNA chip for reindeer.

Keywords: Rangifer tarandus, reindeer, SNP markers, DNA chips.

 

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