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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23874599/?tool=EBI |
| _version_ | 1818389035085725696 |
|---|---|
| author | Joseph I Hoffman Michael A S Thorne Rob McEwing Jaume Forcada Rob Ogden |
| author_facet | Joseph I Hoffman Michael A S Thorne Rob McEwing Jaume Forcada Rob Ogden |
| author_sort | Joseph I Hoffman |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T04:35:19Z |
| format | Article |
| id | doaj.art-168176e9286d4d85a244059610fdef04 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T04:35:19Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-168176e9286d4d85a244059610fdef042022-12-21T23:16:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6836510.1371/journal.pone.0068365Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs.Joseph I HoffmanMichael A S ThorneRob McEwingJaume ForcadaRob OgdenHigh-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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23874599/?tool=EBI |
| spellingShingle | Joseph I Hoffman Michael A S Thorne Rob McEwing Jaume Forcada Rob Ogden Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs. PLoS ONE |
| title | 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_short | 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23874599/?tool=EBI |
| work_keys_str_mv | AT josephihoffman crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT michaelasthorne crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT robmcewing crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT jaumeforcada crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT robogden crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs |