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

Харзинова, В. Р.; Sermyagin, A.A.; Гладырь, Е. А.; Охлопков, И. М.; Brem, Gottfried; Zinovieva, N. A.

doi:10.1093/jhered/esv081

Cited by 20 publications

(32 citation statements)

References 19 publications

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“…In this case the results signalised that the decrease is not so rapid and can reach a level of around 1% per million year divergence. The total number of identifi ed informative polymorphic markers across 50K bovine loci panel at the level of 4.2% was comparable to results presented by Haynes and Latch [19] and Kharzinova et al [20]. Both studies detected using BovineSNP50 BeadChip on approximately 5% of polymorphic loci within the genus Odocoileus and Rangifer.…”

Section: Discussionsupporting

confidence: 83%

“…On the other hand the number of loci detecting by cross-species genotyping is overall too small for reliable analysis of homozygous segments describing the variability across whole genome. In contrast to the study of Kharzinova et al [20] present analyses of genetic diversity and relationship within cervids were based only on parameters that refl ect the allele differences observed within each individual. The power to detect the genetic effects of polymorphic loci depends also on minor allele frequency.…”

Section: Discussionmentioning

confidence: 92%

“…However, most of the current studies assessing phylogeny or population genetics of wild animals require only a reduced set of SNPs that are spread across the genome [7,17,18]. The commercially developed genotyping array for cattle were successfully applied in relation to the novel SNPs detection and validation on two genera from the families Cervidae; Odocoileus [19] and Rangifer [20]. The bovine SNP panel was used to assess the phylogenic relationship between the species from both Bovidae and Cervidae families [21].…”

Section: Introductionmentioning

confidence: 99%

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Genomic variation across cervid species in respect to the estimation of red deer diversity

et al. 2017

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The aim of this study was to assess the genetic variations and relationships across evolutionary related cervid species in order to estimate the genetic diversity of the Red deer population that inhabits the forest area in the south-western part of Slovakia. The study was based on the application of cross-species SNP genotyping. The genomic data were obtained from a total of 86 individuals representing six genera (Axis, Dama, Cervus, Alces, Rangifer, and Odocoileus) using Illumina BovineSNP50 BeadChip. From 38.85% of successfully genotyped loci up to 1,532 SNPs showed polymorphism and were informative for subsequent analyses of the diversity and interspecifi c genetic relationships. Generally, a good level of observed heterozygosity was found across all species. The value of F IS (0.23±0.13) signalised the increase of a homozygous proportion within them. The application of molecular variance analysis to the hierarchical population structure showed that most of the variation was conserved within separate species (96%). The performed diversity analysis of Slovak Red deer population and comparative analysis of their phylogenic relationships among subspecies from genus Cervus did not identify a remarkable loss of genetic variability. Also, were not identifi ed any degree of admixture that could be due to the historical background of deer farming in Slovakia or reintroduction and hybridisation by other species from genus Cervus (C.canadensis, and C. nippon) which are the major risk of loss of autochthonous Red deer populations in many areas of Central Europe. The analysis of individual's ancestry showed consistent results with patterns of evaluated group differentiations which means low migration rates among all species.

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Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Genomic variation across cervid species in respect to the estimation of red deer diversity

et al. 2017

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“…However, this species is highly inbred and has low genetic diversity [18]. Study of other wild-domestic species pairs may therefore provide a more nuanced picture of genomic regions under selection, for example, in domestic pigs and wild boar, or captive and free-living populations of the wild boar (e.g., [24]), thus taking advantage of recent developments in high-density genomic arrays to investigate domestic and wild species (e.g., [25]).…”

Section: Discussionmentioning

confidence: 99%

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

Iacolina

Strønen

Pertoldi

et al. 2016

International Journal of Genomics

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Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.

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“…The number of identified informative loci was comparable to results presented by Wu et al (2013) that similarly used cross-species genotyping to evolutionary related water buffalo. Relative higher proportion of polymorphic SNPs at level of 5% found Hayes and Latch (2012) and Kharzinova et al(2015) within the species Odocoileus virginianus and Rangifer tarandus, respectively. However, the results of cross-species genotyping have to be described with cation mainly due to the differences between cervid and bovid genome that resulted in favour of conserved genomic regions that still retain polymorphisms ancestral to the divergence between Cervidae and Bovidae families (Haynes and Latch, 2012).…”

Section: Resultsmentioning

confidence: 89%

The Degree of Genetic Admixture Within Species From Genus Cervus

Moravčíková¹,

Kasarda²,

Kadlečík³

2017

AgricultForest

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SUMMARYThe aim of present study is to estimate the level of admixture within species originating from genus Cervus (family Cervidae) that can reflect not only their phylogeny origin, but mainly the impact of introgression and hybridization in Red deer population inhabit the forest area of Slovakia. It was happened over the last few centuries. Recently, the introduction and hybridization by non-native species is considered as the major risk of diversity loss within autochthonous Red deer populations in area of Central Europe. The genomic data were obtained from in total 61 animals (species A. axis, D. dama, C. elaphus, C. Nippon, C. canadensis) based on applying the cross-species SNP genotyping (Illumina BovineSNP50 BeadChip). The quality control of genotyping data has been performed to eliminate any SNPs with genotyping errors (loci with >10% missing genotypes), less informative markers (MAF<0.01) and markers deviating from Hardy-Weinberg equilibrium limit of 0.0001. From totally 43.21% of successfully genotyped markers up to 843 were informative for subsequent estimation. As expected the presence of admixed individuals was found within Red deer and Wapiti populations, but the signal of cross-species admixture was low. The membership probabilities of individuals were higher than 90% within each of analysed cervid group. Our study showed that the Slovak Red deer population can provide valuable gene pool within Central European deer populations in respect to the management of genetic resources conservation strategies.

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

Cited by 20 publications

References 19 publications

Genomic variation across cervid species in respect to the estimation of red deer diversity

Genomic variation across cervid species in respect to the estimation of red deer diversity

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

The Degree of Genetic Admixture Within Species From Genus Cervus

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