The development of a genome wide SNP set for the Barnacle goose Branta leucopsis.
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 p...
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ftdoajarticles:oai:doaj.org/article:b22f3264722c4077a45197cfdd4623ba 2023-05-15T15:39:21+02:00 The development of a genome wide SNP set for the Barnacle goose Branta leucopsis. Rudy M Jonker Qiong Zhang Pim Van Hooft Maarten J J E Loonen Henk P Van der Jeugd Richard P M A Crooijmans Martien A M Groenen Herbert H T Prins Robert H S Kraus 2012-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0038412 https://doaj.org/article/b22f3264722c4077a45197cfdd4623ba EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC3393723?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0038412 https://doaj.org/article/b22f3264722c4077a45197cfdd4623ba PLoS ONE, Vol 7, Iss 7, p e38412 (2012) Medicine R Science Q article 2012 ftdoajarticles https://doi.org/10.1371/journal.pone.0038412 2022-12-30T22:55:38Z 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. Article in Journal/Newspaper Barnacle goose Branta leucopsis Directory of Open Access Journals: DOAJ Articles PLoS ONE 7 7 e38412 |
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topic |
Medicine R Science Q |
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Medicine R Science Q Rudy M Jonker Qiong Zhang Pim Van Hooft Maarten J J E Loonen Henk P Van der Jeugd Richard P M A Crooijmans Martien A M Groenen Herbert H T Prins Robert H S Kraus The development of a genome wide SNP set for the Barnacle goose Branta leucopsis. |
topic_facet |
Medicine R Science Q |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Rudy M Jonker Qiong Zhang Pim Van Hooft Maarten J J E Loonen Henk P Van der Jeugd Richard P M A Crooijmans Martien A M Groenen Herbert H T Prins Robert H S Kraus |
author_facet |
Rudy M Jonker Qiong Zhang Pim Van Hooft Maarten J J E Loonen Henk P Van der Jeugd Richard P M A Crooijmans Martien A M Groenen Herbert H T Prins Robert H S Kraus |
author_sort |
Rudy M Jonker |
title |
The development of a genome wide SNP set for the Barnacle goose Branta leucopsis. |
title_short |
The development of a genome wide SNP set for the Barnacle goose Branta leucopsis. |
title_full |
The development of a genome wide SNP set for the Barnacle goose Branta leucopsis. |
title_fullStr |
The development of a genome wide SNP set for the Barnacle goose Branta leucopsis. |
title_full_unstemmed |
The development of a genome wide SNP set for the Barnacle goose Branta leucopsis. |
title_sort |
development of a genome wide snp set for the barnacle goose branta leucopsis. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2012 |
url |
https://doi.org/10.1371/journal.pone.0038412 https://doaj.org/article/b22f3264722c4077a45197cfdd4623ba |
genre |
Barnacle goose Branta leucopsis |
genre_facet |
Barnacle goose Branta leucopsis |
op_source |
PLoS ONE, Vol 7, Iss 7, p e38412 (2012) |
op_relation |
http://europepmc.org/articles/PMC3393723?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0038412 https://doaj.org/article/b22f3264722c4077a45197cfdd4623ba |
op_doi |
https://doi.org/10.1371/journal.pone.0038412 |
container_title |
PLoS ONE |
container_volume |
7 |
container_issue |
7 |
container_start_page |
e38412 |
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