Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs

Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R (2013)
PLoS ONE 8(7).

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Abstract
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.
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Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
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Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE. 2013;8(7).
Hoffman, J., Thorne, M. A. S., McEwing, R., Forcada, J., & Ogden, R. (2013). Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE, 8(7).
Hoffman, J., Thorne, M. A. S., McEwing, R., Forcada, J., and Ogden, R. (2013). Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE 8.
Hoffman, J., et al., 2013. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE, 8(7).
J. Hoffman, et al., “Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs”, PLoS ONE, vol. 8, 2013.
Hoffman, J., Thorne, M.A.S., McEwing, R., Forcada, J., Ogden, R.: Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE. 8, (2013).
Hoffman, Joseph, Thorne, Michael A. S., McEwing, Rob, Forcada, Jaume, and Ogden, Rob. “Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs”. PLoS ONE 8.7 (2013).
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53 References

Data provided by Europe PubMed Central.

RADSeq: next-generation population genetics.
Davey JW, Davey JL, Blaxter ML, Blaxter MW., Brief Funct Genomics 9(5-6), 2010
PMID: 21266344
Gene mapping in the wild with SNPs: guidelines and future directions.
Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton JM., Genetica 136(1), 2009
PMID: 18780148

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