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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ftzenodo:oai:zenodo.org:4999508 2023-06-06T11:54:39+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. 2014-09-04 https://zenodo.org/record/4999508 https://doi.org/10.5061/dryad.b35td unknown doi:10.1111/1755-0998.12327 https://zenodo.org/communities/dryad https://zenodo.org/record/4999508 https://doi.org/10.5061/dryad.b35td oai:zenodo.org:4999508 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Animalia Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene info:eu-repo/semantics/other dataset 2014 ftzenodo https://doi.org/10.5061/dryad.b35td10.1111/1755-0998.12327 2023-04-13T20:43:48Z 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 Hudson Bay polar bear Ursus maritimus Zenodo Hudson Hudson Bay |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
Animalia Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene |
spellingShingle |
Animalia Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene 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 Carnivora Chordata Next-generation sequencing Ursidae Ursus maritimus Mammalia polar bear Ursus Infinium BeadChip single-nucleotide polymorphism Holocene |
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 |
publishDate |
2014 |
url |
https://zenodo.org/record/4999508 https://doi.org/10.5061/dryad.b35td |
geographic |
Hudson Hudson Bay |
geographic_facet |
Hudson Hudson Bay |
genre |
Hudson Bay polar bear Ursus maritimus |
genre_facet |
Hudson Bay polar bear Ursus maritimus |
op_relation |
doi:10.1111/1755-0998.12327 https://zenodo.org/communities/dryad https://zenodo.org/record/4999508 https://doi.org/10.5061/dryad.b35td oai:zenodo.org:4999508 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.b35td10.1111/1755-0998.12327 |
_version_ |
1767961173839314944 |