Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing
Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are n...
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ftdans:oai:easy.dans.knaw.nl:easy-dataset:86091 2023-07-02T03:32:31+02:00 Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing Malenfant, René M. Coltman, David W. Davis, Corey S. 2014-09-04T18:06:49.000+02:00 http://nbn-resolving.org/urn:nbn:nl:ui:13-dt-9i7r https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:86091 unknown doi:10.5061/dryad.b35td/2 doi:10.1111/1755-0998.12327 PMID:25187336 http://nbn-resolving.org/urn:nbn:nl:ui:13-dt-9i7r doi:10.5061/dryad.b35td https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:86091 OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf Life sciences medicine and health care 2014 ftdans https://doi.org/10.5061/dryad.b35td/210.1111/1755-0998.1232710.5061/dryad.b35td 2023-06-13T12:39:12Z Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large-scale genotyping of SNPs remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: (i) the fine-scale population structure among Canadian polar bears and (ii) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction-site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. Six-thousand RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and – after genotyping 1450 polar bears – 5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals and that these results are not driven by the SNP ascertainment scheme. Here, we present one of the first large-scale genotyping resources designed for a threatened species. Other/Unknown Material Hudson Bay Ursus maritimus Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) Hudson Hudson Bay |
institution |
Open Polar |
collection |
Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) |
op_collection_id |
ftdans |
language |
unknown |
topic |
Life sciences medicine and health care |
spellingShingle |
Life sciences medicine and health care Malenfant, René M. Coltman, David W. Davis, Corey S. Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing |
topic_facet |
Life sciences medicine and health care |
description |
Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large-scale genotyping of SNPs remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: (i) the fine-scale population structure among Canadian polar bears and (ii) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction-site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. Six-thousand RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and – after genotyping 1450 polar bears – 5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals and that these results are not driven by the SNP ascertainment scheme. Here, we present one of the first large-scale genotyping resources designed for a threatened species. |
author |
Malenfant, René M. Coltman, David W. Davis, Corey S. |
author_facet |
Malenfant, René M. Coltman, David W. Davis, Corey S. |
author_sort |
Malenfant, René M. |
title |
Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing |
title_short |
Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing |
title_full |
Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing |
title_fullStr |
Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing |
title_full_unstemmed |
Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing |
title_sort |
data from: design of a 9k snp chip for polar bears (ursus maritimus) from rad and transcriptome sequencing |
publishDate |
2014 |
url |
http://nbn-resolving.org/urn:nbn:nl:ui:13-dt-9i7r https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:86091 |
geographic |
Hudson Hudson Bay |
geographic_facet |
Hudson Hudson Bay |
genre |
Hudson Bay Ursus maritimus |
genre_facet |
Hudson Bay Ursus maritimus |
op_relation |
doi:10.5061/dryad.b35td/2 doi:10.1111/1755-0998.12327 PMID:25187336 http://nbn-resolving.org/urn:nbn:nl:ui:13-dt-9i7r doi:10.5061/dryad.b35td https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:86091 |
op_rights |
OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf |
op_doi |
https://doi.org/10.5061/dryad.b35td/210.1111/1755-0998.1232710.5061/dryad.b35td |
_version_ |
1770272112529899520 |