Subset of SNPs for parental identification in European bison Lowland-Białowieża line (Bison bonasus bonasus)

Oleński, Kamil; Kamiński, Stanisław; Tokarska, Małgorzata; Hering, Dorota

doi:10.1007/s12686-017-0768-3

Cited by 13 publications

(21 citation statements)

References 13 publications

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“…Commercially developed livestock genotyping arrays have been used in several studies to identify novel SNPs in closely evolutionarily related non-model species [50, 51], including those for the family Cervidae [30, 31; 33]. In our study, a total of 135 domestic and wild reindeer, inhabiting the Nenets Autonomous district, Murmansk region, western Taymyr, and Yakutia, were genotyped with Illumina BovineHD BeadChip.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip

et al. 2018

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Reindeer (Rangifer tarandus L. 1758) are an essential element of the Russian Far North, providing a significant source of nutrition for the representatives of 18 ethnicities. The species has wild and domestic forms, which are in constant interaction. The aim of our study was to characterize the genetic structure of domestic and wild reindeer populations, using a genome-wide bovine genotyping array (BovineHD BeadChip). The wild reindeer samples were obtained from the western Taymyr Peninsula population and from the taiga and tundra populations in the Sakha Republic (Yakutia). The domestic populations included the Evenk, Even, and Chukotka-Khargin breeds of Yakutia and the Nenets breed from the Nenets Autonomous district and Murmansk region. The level of genetic diversity was higher for the wild population. Analyzing Neighbor-Net tree, multidimensional scaling, and Structure results, we observed strong genetic population structure and clear differentiation between domestic and wild populations. All regional populations of domestic reindeer were clearly separated, while wild reindeer showed similar genetic backgrounds. Nevertheless, we found contrasting patterns in the genetic structure of the tundra and taiga reindeer, in accordance with their morphological and ecological differences. Thus, our study revealed a clear genetic differentiation between domestic and wild reindeer populations. It provides novel insights into the genetic diversity and structure of reindeer populations, to support resource utilization and aid in the development of genetic improvement strategies and conservation programs for this species.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip

et al. 2018

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“…Authors showed that SNP genotyping systems developed for domestic species could be effective even in bottlenecked species in which heterozygosity of other markers such as microsatellites may be very low [46,32]. Along with the study of biodiversity and evolutionary relationships, SNP markers have found application for the determination of the parentage verification [47]. Thus, above-mentioned studies clearly showed that SNP genotyping systems developed for domestic species represent powerful tools for genetic analysis in related non-model species Thus, as the result of our study of single nucleotide polymorphisms using DNA chips, designed for cattle, we gave the population-genetic characterization of three breeds of domestic reindeer -Chukotka (Khargin), Even and Evenk, which are bred in the territory of one of the main reindeer herding regions of Russia -Republic of Sakha (Yakutia).…”

Section: Differentiation Of the Studied Breeds Of Reindeermentioning

confidence: 99%

Population-Genetic Characteristics of Domestic Reindeer of Yakutia Based on Whole-Genome SNP Analysis

Харзинова¹,

Dotsev²,

Solovieva³

et al. 2017

S-h. biol.

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A b s t r a c tThe 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 (H o = 0.180±0.011, H e = 0.156±0.008, A r = 1.488±0.022) and a higher excess of heterozygotes (F IS = 0.124), compared to Evenk (H o = 0.161±0.009, H e = 0.153±0.008, A r = 1.487±0.020, and F IS = 0.047) and Even (H o = 0.164±0.010, H e = 0.149±0.008, A r = 1.471±0.021, and F IS = 0.089) breeds. The results of multidimensional scaling and the calculation of pairwise genetic distances (F ST ) 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.

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“…Overall, 27 samples (11 long-lived and 16 reference) were genotyped using the SNP array. According to the previous successful genotyping of bison individuals using bovine SNP chips ( Oleński et al., 2020 ; Oleński, Kamiński, Tokarska & Hering, 2017 ; Stronen et al., 2018 ), we decided to genotype our samples using Illumina BovineHD BeadChip at Neogen laboratory, 4131 N. 48th St. Lincoln, NE 68504, USA. This chip allows analysis of more than 770,000 SNPs.…”

Section: Methodsmentioning

confidence: 99%

Three new genes associated with longevity in the European Bison

Korec

Ungrová

Hejnar

et al. 2022

Veterinary and Animal Science

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Subset of SNPs for parental identification in European bison Lowland-Białowieża line (Bison bonasus bonasus)

Cited by 13 publications

References 13 publications

Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip

Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip

Population-Genetic Characteristics of Domestic Reindeer of Yakutia Based on Whole-Genome SNP Analysis

Three new genes associated with longevity in the European Bison

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