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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Dryad
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Online Access: | https://doi.org/10.5061/dryad.b35td |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::e5910eace89f4cceecd6fe1b81fa1a18 2023-05-15T15:17:36+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. 2021-06-25 https://doi.org/10.5061/dryad.b35td en eng Dryad http://dx.doi.org/10.5061/dryad.b35td https://dx.doi.org/10.5061/dryad.b35td lic_creative-commons 10.5061/dryad.b35td oai:easy.dans.knaw.nl:easy-dataset:86091 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:86091 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Animalia population genetics Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene Life sciences medicine and health care Canada Arctic info geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2021 fttriple https://doi.org/10.5061/dryad.b35td 2023-01-22T17:23:20Z 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. SNP and microsatellite dataRAD, transcriptomic, and microsatellite data used in the manuscript, as well as inputs/outputs of analyses. This archive contains the complete RAD .vcf file. For the complete transcriptomic .vcf file, see doi:10.5061/dryad.606j6, which is described in doi:10.1111/1755-0998.12190.DRYAD.zip Dataset Arctic Hudson Bay polar bear Ursus maritimus Unknown Arctic Hudson Bay Canada Hudson |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
Animalia population genetics Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene Life sciences medicine and health care Canada Arctic info geo |
spellingShingle |
Animalia population genetics Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene Life sciences medicine and health care Canada Arctic info geo 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 |
Animalia population genetics Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene Life sciences medicine and health care Canada Arctic info geo |
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. SNP and microsatellite dataRAD, transcriptomic, and microsatellite data used in the manuscript, as well as inputs/outputs of analyses. This archive contains the complete RAD .vcf file. For the complete transcriptomic .vcf file, see doi:10.5061/dryad.606j6, which is described in doi:10.1111/1755-0998.12190.DRYAD.zip |
format |
Dataset |
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 |
publisher |
Dryad |
publishDate |
2021 |
url |
https://doi.org/10.5061/dryad.b35td |
geographic |
Arctic Hudson Bay Canada Hudson |
geographic_facet |
Arctic Hudson Bay Canada Hudson |
genre |
Arctic Hudson Bay polar bear Ursus maritimus |
genre_facet |
Arctic Hudson Bay polar bear Ursus maritimus |
op_source |
10.5061/dryad.b35td oai:easy.dans.knaw.nl:easy-dataset:86091 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:86091 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.b35td https://dx.doi.org/10.5061/dryad.b35td |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.b35td |
_version_ |
1766347843943006208 |