An 85K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony
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 w...
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ftnerc:oai:nora.nerc.ac.uk:528360 2023-05-15T13:41:45+02:00 An 85K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony Humble, Emily Paijmans, Anneke J. Forcada, Jaume Hoffman, Joseph I. 2020-08-01 text http://nora.nerc.ac.uk/id/eprint/528360/ https://nora.nerc.ac.uk/id/eprint/528360/1/2787.full.pdf https://www.g3journal.org/content/10/8/2787 en eng Genetics Society America https://nora.nerc.ac.uk/id/eprint/528360/1/2787.full.pdf Humble, Emily; Paijmans, Anneke J.; Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. orcid:0000-0001-5895-8949 . 2020 An 85K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony. G3L Genes, Genomes, Genetics, 10 (8). 2787-2799. https://doi.org/10.1534/g3.120.401268 <https://doi.org/10.1534/g3.120.401268> cc_by_4 CC-BY Publication - Article PeerReviewed 2020 ftnerc https://doi.org/10.1534/g3.120.401268 2023-02-04T19:51:03Z 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 Natural Environment Research Council: NERC Open Research Archive Antarctic The Antarctic Bird Island ENVELOPE(-38.060,-38.060,-54.004,-54.004) G3 Genes|Genomes|Genetics 10 8 2787 2799 |
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Open Polar |
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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
language |
English |
description |
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 J. Forcada, Jaume Hoffman, Joseph I. |
spellingShingle |
Humble, Emily Paijmans, Anneke J. Forcada, Jaume Hoffman, Joseph I. An 85K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony |
author_facet |
Humble, Emily Paijmans, Anneke J. Forcada, Jaume Hoffman, Joseph I. |
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 America |
publishDate |
2020 |
url |
http://nora.nerc.ac.uk/id/eprint/528360/ https://nora.nerc.ac.uk/id/eprint/528360/1/2787.full.pdf https://www.g3journal.org/content/10/8/2787 |
long_lat |
ENVELOPE(-38.060,-38.060,-54.004,-54.004) |
geographic |
Antarctic The Antarctic Bird Island |
geographic_facet |
Antarctic The Antarctic Bird Island |
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 |
https://nora.nerc.ac.uk/id/eprint/528360/1/2787.full.pdf Humble, Emily; Paijmans, Anneke J.; Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. orcid:0000-0001-5895-8949 . 2020 An 85K SNP array uncovers inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony. G3L Genes, Genomes, Genetics, 10 (8). 2787-2799. https://doi.org/10.1534/g3.120.401268 <https://doi.org/10.1534/g3.120.401268> |
op_rights |
cc_by_4 |
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 |
_version_ |
1766157013092401152 |