Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs
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 genotyp...
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ftpubmed:oai:pubmedcentral.nih.gov:3712990 2023-05-15T13:56:37+02:00 Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs Hoffman, Joseph I. Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob 2013-07-16 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712990 http://www.ncbi.nlm.nih.gov/pubmed/23874599 https://doi.org/10.1371/journal.pone.0068365 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712990 http://www.ncbi.nlm.nih.gov/pubmed/23874599 http://dx.doi.org/10.1371/journal.pone.0068365 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2013 ftpubmed https://doi.org/10.1371/journal.pone.0068365 2013-09-05T02:33:42Z 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. Text Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella PubMed Central (PMC) Antarctic PLoS ONE 8 7 e68365 |
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Research Article Hoffman, Joseph I. Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
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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. |
format |
Text |
author |
Hoffman, Joseph I. Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob |
author_facet |
Hoffman, Joseph I. Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob |
author_sort |
Hoffman, Joseph I. |
title |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_short |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_full |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_fullStr |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_full_unstemmed |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_sort |
cross-amplification and validation of snps conserved over 44 million years between seals and dogs |
publisher |
Public Library of Science |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712990 http://www.ncbi.nlm.nih.gov/pubmed/23874599 https://doi.org/10.1371/journal.pone.0068365 |
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Antarctic |
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Antarctic |
genre |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712990 http://www.ncbi.nlm.nih.gov/pubmed/23874599 http://dx.doi.org/10.1371/journal.pone.0068365 |
op_rights |
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
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CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0068365 |
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e68365 |
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