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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Autores principales:	Joseph I Hoffman, Michael A S Thorne, Rob McEwing, Jaume Forcada, Rob Ogden
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/168176e9286d4d85a244059610fdef04
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spelling	oai:doaj.org-article:168176e9286d4d85a244059610fdef042021-11-18T07:37:35ZCross-amplification and validation of SNPs conserved over 44 million years between seals and dogs.1932-620310.1371/journal.pone.0068365https://doaj.org/article/168176e9286d4d85a244059610fdef042013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23874599/?tool=EBIhttps://doaj.org/toc/1932-6203High-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.Joseph I HoffmanMichael A S ThorneRob McEwingJaume ForcadaRob OgdenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68365 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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.
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.
format	article
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
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 (PLoS)
publishDate	2013
url	https://doaj.org/article/168176e9286d4d85a244059610fdef04
work_keys_str_mv	AT josephihoffman crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT michaelasthorne crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT robmcewing crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT jaumeforcada crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs AT robogden crossamplificationandvalidationofsnpsconservedover44millionyearsbetweensealsanddogs
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Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs.

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