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Senn H.,WildGenes Laboratory | Ogden R.,WildGenes Laboratory | Cezard T.,University of Edinburgh | Gharbi K.,University of Edinburgh | And 5 more authors.
Molecular Ecology | Year: 2013

In this study, we used restriction site-associated DNA (RAD) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the Eurasian beaver (Castor fibre) to Scotland. In the absence of a reference genome for beaver, we built contigs and discovered SNPs within them using paired-end RAD data, so as to have sufficient flanking region around the SNPs to conduct marker design. To do this, we used a simple pipeline which catalogued the Read 1 data in stacks and then used the assembler cortex-var to conduct de novo assembly and genotyping of multiple samples using the Read 2 data. The analysis of around 1.1 billion short reads of sequence data was reduced to a set of 2579 high-quality candidate SNP markers that were polymorphic in Norwegian and Bavarian beaver. Both laboratory validation of a subset of eight of the SNPs (1.3% error) and internal validation by confirming patterns of Mendelian inheritance in a family group (0.9% error) confirmed the success of this approach. © 2013 John Wiley & Sons Ltd.


Wilkinson S.,Roslin Institute | Wilkinson S.,Scotland’s Rural College | Archibald A.L.,Roslin Institute | Haley C.S.,Roslin Institute | And 6 more authors.
BMC Genomics | Year: 2012

Background: The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom.Results: The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity.Conclusion: The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics. © 2012 2012 Wilkinson et al.; licensee BioMed Central Ltd.


Wilkinson S.,Roslin Institute | Wilkinson S.,Scotland’s Rural College | Lu Z.H.,Roslin Institute | Megens H.-J.,Wageningen University | And 9 more authors.
PLoS Genetics | Year: 2013

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition. © 2013 Wilkinson et al.


Gharbi K.,University of Edinburgh | Mugue N.,Russian Institute for Fisheries and Oceanography VNIRO | Martinsohn J.,European Commission - Joint Research Center Ispra | Senn H.,WildGenes Laboratory | And 6 more authors.
Molecular Ecology | Year: 2013

Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping-by-sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools. © 2013 John Wiley & Sons Ltd.


Hoffman J.I.,Bielefeld University | Thorne M.A.S.,Natural Environment Research Council | McEwing R.,Wildgenes Laboratory | Forcada J.,Natural Environment Research Council | Ogden R.,Wildgenes Laboratory
PLoS ONE | Year: 2013

High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome. © 2013 Hoffman et al.


Ogden R.,Wildgenes Laboratory | Baird J.,Gen-Probe | Senn H.,Wildgenes Laboratory | McEwing R.,Wildgenes Laboratory
Conservation Genetics Resources | Year: 2012

The potential use of single nucleotide polymorphism markers (SNPs) in conservation genetics is widely recognized; however, methods for discovering large numbers of SNPs typically rely on relatively expensive, genome-wide, species-specific research projects which limits their development in many taxa. Here we describe the use of high-density SNP genotyping arrays designed for cattle to discover SNPs in two antelope species. From a total of 54,001 SNP markers on the array, the analysis yielded 148 polymorphic markers in the scimitar-horned oryx and 149 in the Arabian oryx. The results represent a first step toward developing SNP marker panels for ongoing projects on each species. As high density genotyping arrays become available for an increasing number of model species, this approach has the potential to generate SNP markers, rapidly and affordably, in a broad range of species for conservation genetic research. © 2011 Springer Science+Business Media B.V.


Mellanby R.J.,Roslin Institute | Ogden R.,WildGenes Laboratory | Clements D.N.,Roslin Institute | French A.T.,Roslin Institute | And 5 more authors.
Veterinary Journal | Year: 2013

There is increasing concern that reproductive isolation related to breed specifications in dogs, while maintaining genetic differences among breeds, is likely to promote breed-specific genetic disorders. This study examined genetic diversity among 13 popular dog breed groups in the UK. Most breeds showed high levels of homozygosity when compared with crossbred animals. The Boxer and West Highland white terrier showed the lowest heterozygosity, while the Jack Russell terrier group (not a registered breed in the UK) had a level of heterozygosity comparable to crossbred dogs. Analysis of genetic distance between breeds showed significantly different inbreeding coefficients for pairwise comparisons among registered breeds, with the most divergent breeds being the Boxer and West Highland white terrier. The Rottweiler and Golden retriever showed the highest levels of inbreeding. The least distinct group contained crossbred dogs. The results show that the registered breeds are subject to a 'breed barrier' which promotes reduction in genetic diversity. © 2012 Elsevier Ltd.


Alqamy H.E.,Environmental Agency | Senn H.,WildGenes Laboratory | Roberts M.-F.,WildGenes Laboratory | McEwing R.,WildGenes Laboratory | Ogden R.,WildGenes Laboratory
Conservation Genetics | Year: 2012

Since being declared extinct in the wild in 1972, the Arabian oryx has been the subject of intense and sustained effort to maintain a healthy captive population and to reintroduce the species to its ancestral range. Previous reintroductions and associated genetic assessments focused on the release of closely managed zoo animals into Oman and included observations of inbreeding and outbreeding depression. Here we describe the use of multiple unmanaged herds as source populations for a new reintroduction project in the United Arab Emirates, allowing a comparison between studbook management and uncontrolled semi-captive breeding approaches to the conservation of genetic diversity. Results of mitochondrial control region sequencing and 13-locus microsatellite profiling highlight a severe lack of diversity within individual source populations, but a level of differentiation among populations that supports the formation of a mixed founder herd. The combined release group contained a similar level of diversity to each of the intensively managed captive populations. The research includes the first genetic data for animals held on Sir Bani Yas Island, a former private reserve which until recently held over 50% of the world's Arabian and scimitar-horned oryx and is recognized as having huge potential for re-establishing endangered antelope species in the wild. The genetic assessment provides the first stage of an ongoing genetic monitoring programme to support future supplemental releases, translocations and genetic management of reintroduced populations. © 2011 Springer Science+Business Media B.V.


Wilkinson S.,Roslin Institute | Wiener P.,Roslin Institute | Archibald A.L.,Roslin Institute | Law A.,Roslin Institute | And 4 more authors.
BMC Genetics | Year: 2011

Background: Genetic markers can be used to identify and verify the origin of individuals. Motivation for the inference of ancestry ranges from conservation genetics to forensic analysis. High density assays featuring Single Nucleotide Polymorphism (SNP) markers can be exploited to create a reduced panel containing the most informative markers for these purposes. The objectives of this study were to evaluate methods of marker selection and determine the minimum number of markers from the BovineSNP50 BeadChip required to verify the origin of individuals in European cattle breeds. Delta, Wright's FST, Weir & Cockerham's FSTand PCA methods for population differentiation were compared. The level of informativeness of each SNP was estimated from the breed specific allele frequencies. Individual assignment analysis was performed using the ranked informative markers. Stringency levels were applied by log-likelihood ratio to assess the confidence of the assignment test.Results: A 95% assignment success rate for the 384 individually genotyped animals was achieved with < 80, < 100, < 140 and < 200 SNP markers (with increasing stringency threshold levels) across all the examined methods for marker selection. No further gain in power of assignment was achieved by sampling in excess of 200 SNP markers. The marker selection method that required the lowest number of SNP markers to verify the animal's breed origin was Wright's FST(60 to 140 SNPs depending on the chosen degree of confidence). Certain breeds required fewer markers (< 100) to achieve 100% assignment success. In contrast, closely related breeds require more markers (~200) to achieve > 95% assignment success. The power of assignment success, and therefore the number of SNP markers required, is dependent on the levels of genetic heterogeneity and pool of samples considered.Conclusions: While all SNP selection methods produced marker panels capable of breed identification, the power of assignment varied markedly among analysis methods. Thus, with effective exploration of available high density genetic markers, a diagnostic panel of highly informative markers can be produced. © 2011 Wilkinson et al; licensee BioMed Central Ltd.


McEwing R.,WildGenes Laboratory | Frosch C.,Senckenberg Institute | Rosell F.,Telemark University College | Campbell-Palmer R.,Telemark University College
European Journal of Wildlife Research | Year: 2014

The confirmed presence of alien North American beavers in some regions of Eurasia may compete with and hinder the successful recolonisation of the native Eurasian species back to its former range. Distinguishing the two species in the field can be problematic, time consuming and expensive, thereby potentially limiting appropriate conservation actions. Here, a rapid and inexpensive genetic SNP assay is described that can separate the two species from either non-invasively collected samples or samples taken directly from restrained individuals. We applied these new genetic assays to free-living beavers of unknown origin sampled in Scotland. © 2014 Springer-Verlag Berlin Heidelberg.

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