ArticlePloS one2013
Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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Who cites it
9 citing papers in PubMed, 24 citations in OpenAlex.
- Review
- Application potential of chicken DNA chip in domestic pigeon species - Preliminary results.Saudi journal of biological sciences · 2023Article
- An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony.G3 (Bethesda, Md.) · 2020Article
- Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse.Scientific reports · 2019Article
- Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip.Frontiers in genetics · 2019Article
- RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding.G3 (Bethesda, Md.) · 2018Article
- Strategies for determining kinship in wild populations using genetic data.Ecology and evolution · 2016Review
- Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity.The Journal of heredity · 2016Article
- Response to "Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity" by Shafer, Miller, and Kardos.The Journal of heredity · 2016Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.