Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Haynes, Gwilym D.; Latch, Emily K.

doi:10.1371/journal.pone.0036536

Cited by 62 publications

(62 citation statements)

References 76 publications

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“…The average values of MAF for both analysed cattle breeds were lower than the mean values reported for taurine breeds (Boichard et al, 2012;Wiggans et al, 2012). The value found for Zebu and cervids was comparable with results reported by Mustafa et al (2014) and Haynes and Latch (2012), respectively. The variations in values of MAFs in presented results and previous studies could be caused by different densities of SNPs on the used genotyping arrays.…”

Section: Resultssupporting

confidence: 87%

“…Only few studies so far have utilized commercially developed SNP arrays for genotyping more phylogenetically distant species (Decker et al, 2009;Haynes and Latch, 2012;Miller et al, 2012;Hoffman et al, 2013). Since the initial genotyping array has a large enough number of loci, even a low proportion of cross-amplifying SNPs may represent a useful set of markers for species which lack genomic resources (Hoffman et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

“…The application of SNPs in population genetics studies of non-model organisms can be difficult due to the absence of genomic resources (Seeb et al, 2011). However recent studies have shown that the high-density SNP array development for livestock species such as cattle, sheep and horse can be successfully used in closely related and also phylogenetically more distant non-model species, in which they can yield large numbers of markers for relatively modest technical efforts and expenditure (Pertoldi et al, 2010;Haynes and Latch, 2012;Miller et al, 2012;Hoffman et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip

et al. 2015

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Abstract. This study presents the application of BovineSNP50 BeadChip for genome-wide screening of two taurine breeds (Bos primigenius taurus) and Zebu (Bos primigenius indicus), and two species from the family Cervidae: red deer (Cervus elaphus) and fallow deer (Dama dama). The aim of the paper was to evaluate the use of bovine array for cross-species genotyping and analyse single nucleotide polymorphism (SNP) distribution, diversity within groups of animals and genetic distance among analysed species. The number of polymorphic SNPs decreased with the increase of phylogenetic distance between species, which also reflected a decrease in call rate (from 99.54 to 61.19 %). The minor allele frequency (MAF) values were significantly different between species and ranged from 0.18 ± 15 (Zebu) to 0.26 ± 0.14 (Pinzgau). The subsequent analyses of genetic diversity were based on the polymorphic loci detected in cervids. Differences in the expected heterozygosity was low (0.06), on average 0.34. In analysed groups the F IS values were close to zero, which suggested low SNP variance within them. The value of F IT indicated homozygote excess in evaluated individuals. Analysis of molecular variance revealed that most of the variability was distributed within all individuals. Observed genetic distances within and across groups of animals suggested that taurine cattle and cervids were more distant. The study results showed that genotyping array prepared for model species can be applied not only to organisms for which was developed, but can be also successfully used in closely related and more phylogenetically divergent species.

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip

et al. 2015

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“…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: 99%

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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“…To date, commercially developed livestock genotyping arrays have been used in several studies to identify novel SNPs in closely evolutionarily related non-model species (Miller et al 2011, Wu et al 2013, including those from the family Cervidae (Bixley et al 2009, Decker et al 2009, Haynes and Latch 2012. The successful detection of novel SNPs applicable for population studies of non-model organisms using cross-species genotyping depends on the genetic divergence among species (Miller et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Suitability of BovineSNP50 BeadChip for the evaluation of the Cervidae family diversity

Kasarda¹,

Moravčíková²,

Šidlová³

et al. 2015

CZECH J ANIM SCI

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Polymorphic SNPs were identified using BovineSNP50 BeadChip in three groups of cervids: farmed Red deer (n = 3), and free range Red deer (n = 5) and Fallow deer (n = 2). From the total of 54 609 SNPs, 53.85% could be genotyped. Out of 28 502 successfully genotyped autosomal SNPs only 5.3% were polymorphic. The average minor allele frequency within cervids was 0.23 (number of polymorphic SNPs ranged from 467 to 686). Results of the molecular variance analysis showed that 67.38% of variation occurred within individuals and the rest was explained by a species difference (F ST = 0.32). The value of F IT (0.33) indicated a higher proportion of homozygote genotypes in the analyzed dataset. Pairwise F ST values showed very clearly the genetic differentiation between Red and Fallow deer which ranged from 0.06 (farmed and free range deer) to 0.74 (farmed Red and Fallow deer). A similar result was found for Nei's genetic distances that ranged from 0.01 (among Fallow deer) to 0.79 (among farmed Red and Fallow deer). The genetic differentiation of the analyzed cervid species was evaluated also by the principal component analysis with the involvement of 6 other species from the family Cervidae, which showed a division of the Cervidae cluster into 7 subpopulations. The panels of SNPs primarily produced for a model species are becoming the marker of choice for the application in other species, but the best methods of their discovery, validation, and genotyping in non-model species need further investigations.

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Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Cited by 62 publications

References 76 publications

Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip

Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip

The Degree of Genetic Admixture Within Species From Genus Cervus

Suitability of BovineSNP50 BeadChip for the evaluation of the Cervidae family diversity

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