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 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.