ArticlePloS one2012
The development of a genome wide SNP set for the Barnacle goose Branta leucopsis.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Article
- Flyway structure in the circumpolar greater white-fronted goose.Ecology and evolution · 2018Article
- Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays.Scientific reports · 2017Article
- Population-level consequences of complementary sex determination in a solitary parasitoid.BMC evolutionary biology · 2015Article
- Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.BMC genomics · 2014Article
- Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays.International journal of molecular sciences · 2013Article
- Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar).BMC genomics · 2013Article
- Circannual transitions in gene expression: lessons from seasonal adaptations.Current topics in developmental biology · 2013Review
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Authors and funding
9 authors.
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Abstract
Migratory birds are of particular interest for population genetics because of the high connectivity between habitats and populations. A high degree of connectivity requires using many genetic markers to achieve the required statistical power, and a genome wide SNP set can fit this purpose. Here we present the development of a genome wide SNP set for the Barnacle Goose Branta leucopsis, a model species for the study of bird migration. We used the genome of a different waterfowl species, Mallard Anas platyrhynchos, as a reference to align Barnacle Goose second generation sequence reads from an RRL library and detected 2188 SNPs genome wide. Furthermore, we used chimeric flanking sequences, merged from both Mallard and Barnacle Goose DNA sequence information, to create primers for validation by genotyping. Validation with a 384 SNP genotyping set resulted in 374 (97%) successfully typed SNPs in the assay, of which 358 (96%) were polymorphic. Additionally, we validated our SNPs on relatively old (30 years) museum samples, which resulted in a success rate of at least 80%. This shows that museum samples could be used in standard SNP genotyping assays. Our study also shows that the genome of a related species can be used as reference to detect genome wide SNPs in birds, because genomes of birds are highly conserved. This is illustrated by the use of chimeric flanking sequences, which showed that the incorporation of flanking nucleotides from Mallard into Barnacle Goose sequences lead to equal genotyping performance when compared to flanking sequences solely composed of Barnacle Goose sequence.
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