An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony
Humble E, Paijmans A, Forcada J, Hoffman J. An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3: Genes, Genomes, Genetics . 2020;10(8):2787-2799. High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be ra...
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Genetics Society of America
2020
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Online Access: | https://nbn-resolving.org/urn:nbn:de:0070-pub-29452568 https://pub.uni-bielefeld.de/record/2945256 https://pub.uni-bielefeld.de/download/2945256/2945259 |
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ftubbiepub:oai:pub.uni-bielefeld.de:2945256 2023-05-15T13:40:40+02:00 An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony Humble, Emily Paijmans, Anneke Forcada, Jaume Hoffman, Joseph 2020 https://nbn-resolving.org/urn:nbn:de:0070-pub-29452568 https://pub.uni-bielefeld.de/record/2945256 https://pub.uni-bielefeld.de/download/2945256/2945259 eng eng Genetics Society of America info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.120.401268 info:eu-repo/semantics/altIdentifier/issn/2160-1836 info:eu-repo/semantics/altIdentifier/wos/000560448200020 info:eu-repo/semantics/altIdentifier/pmid/32540866 https://nbn-resolving.org/urn:nbn:de:0070-pub-29452568 https://pub.uni-bielefeld.de/record/2945256 https://pub.uni-bielefeld.de/download/2945256/2945259 https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess CC-BY Genetics(clinical) Genetics Molecular Biology ddc:590 http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article doc-type:article text 2020 ftubbiepub https://doi.org/10.1534/g3.120.401268 2022-02-08T22:37:08Z Humble E, Paijmans A, Forcada J, Hoffman J. An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3: Genes, Genomes, Genetics . 2020;10(8):2787-2799. High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Antarctic Fur Seals Arctocephalus gazella Bird Island PUB - Publications at Bielefeld University Antarctic Bird Island ENVELOPE(-38.060,-38.060,-54.004,-54.004) The Antarctic G3 Genes|Genomes|Genetics 10 8 2787 2799 |
institution |
Open Polar |
collection |
PUB - Publications at Bielefeld University |
op_collection_id |
ftubbiepub |
language |
English |
topic |
Genetics(clinical) Genetics Molecular Biology ddc:590 |
spellingShingle |
Genetics(clinical) Genetics Molecular Biology ddc:590 Humble, Emily Paijmans, Anneke Forcada, Jaume Hoffman, Joseph An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony |
topic_facet |
Genetics(clinical) Genetics Molecular Biology ddc:590 |
description |
Humble E, Paijmans A, Forcada J, Hoffman J. An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3: Genes, Genomes, Genetics . 2020;10(8):2787-2799. High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community. |
format |
Article in Journal/Newspaper |
author |
Humble, Emily Paijmans, Anneke Forcada, Jaume Hoffman, Joseph |
author_facet |
Humble, Emily Paijmans, Anneke Forcada, Jaume Hoffman, Joseph |
author_sort |
Humble, Emily |
title |
An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony |
title_short |
An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony |
title_full |
An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony |
title_fullStr |
An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony |
title_full_unstemmed |
An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony |
title_sort |
85k snp array uncovers inbreeding and cryptic relatedness in an antarctic fur seal breeding colony |
publisher |
Genetics Society of America |
publishDate |
2020 |
url |
https://nbn-resolving.org/urn:nbn:de:0070-pub-29452568 https://pub.uni-bielefeld.de/record/2945256 https://pub.uni-bielefeld.de/download/2945256/2945259 |
long_lat |
ENVELOPE(-38.060,-38.060,-54.004,-54.004) |
geographic |
Antarctic Bird Island The Antarctic |
geographic_facet |
Antarctic Bird Island The Antarctic |
genre |
Antarc* Antarctic Antarctic Fur Seal Antarctic Fur Seals Arctocephalus gazella Bird Island |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Antarctic Fur Seals Arctocephalus gazella Bird Island |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.120.401268 info:eu-repo/semantics/altIdentifier/issn/2160-1836 info:eu-repo/semantics/altIdentifier/wos/000560448200020 info:eu-repo/semantics/altIdentifier/pmid/32540866 https://nbn-resolving.org/urn:nbn:de:0070-pub-29452568 https://pub.uni-bielefeld.de/record/2945256 https://pub.uni-bielefeld.de/download/2945256/2945259 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.120.401268 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
10 |
container_issue |
8 |
container_start_page |
2787 |
op_container_end_page |
2799 |
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1766138336234176512 |