Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs

Hoffman, Joseph I.; Thorne, Michael A. S. ORCID: https://orcid.org/0000-0001-7759-612X; McEwing, Rob; Forcada, Jaume ORCID: https://orcid.org/0000-0002-2115-0150; Ogden, Rob. 2013 Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs. PLoS ONE, 8 (7). e68365. https://doi.org/10.1371/journal.pone.0068365

Before downloading, please read NORA policies.

Preview

Text (Open access article made available under a CC-BY Creative Commons Attribution license.)
journal.pone.0068365.pdf - Published Version
Download (1MB) | Preview

Abstract/Summary

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.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1371/journal.pone.0068365
Programmes:	BAS Programmes > Polar Science for Planet Earth (2009 - ) > Ecosystems
ISSN:	1932-6203
Additional Keywords:	Single nucleotide polymorphisms, population genetics, fur seal, genotyping
Date made live:	17 Jul 2013 11:25 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/502656

Item Type:

Publication - Article

Digital Object Identifier (DOI):

https://doi.org/10.1371/journal.pone.0068365

Programmes:

BAS Programmes > Polar Science for Planet Earth (2009 - ) > Ecosystems

ISSN:

1932-6203

Additional Keywords:

Single nucleotide polymorphisms, population genetics, fur seal, genotyping

Date made live:

17 Jul 2013 11:25 +0 (UTC)