Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing ...

• Main Authors: Malenfant, René M., Coltman, David W., Davis, Corey S.
• Format: Dataset
• Language: English
• Published: Dryad 2014
• Subjects: Animalia; Carnivora; Chordata; Next-generation sequencing; Ursidae; Ursus maritimus; Mammalia; polar bear; Ursus; Infinium BeadChip; single-nucleotide polymorphism; Holocene; Hudson; Hudson Bay
• Online Access: https://dx.doi.org/10.5061/dryad.b35td; https://datadryad.org/stash/dataset/doi:10.5061/dryad.b35td

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 ... : 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 ...