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.

单核苷酸多态性（single-nucleotide polymorphisms, SNPs）相较于微卫星等匿名分子标记具备诸多优势，包括可更精准地估算种群参数、更细致地解析种群遗传结构，以及对数量性状开展更精确的基因组层面剖析。不过，要达到单个微卫星标记的分辨能力，需要使用多个SNPs；且在非模式生物中，实现可靠的大规模SNP基因分型仍是一项挑战。在此，我们报道一款针对北极熊（Ursus maritimus）开发的9K Illumina Infinium芯片，该芯片将用于两项研究：其一为解析加拿大北极熊种群的精细遗传结构，其二为探究西哈德逊湾亚群的表型性状基因组架构。为此，我们对分布于环北极区域的38只北极熊开展了限制性酶切位点相关DNA（restriction-site associated DNA, RAD）测序，同时对来自西哈德逊湾亚群的10只个体进行了血液与脂肪转录组测序。我们分别主要基于基因组间距与基因功能，为该芯片筛选出了6000个RAD相关SNPs与3000个转录组SNPs。从Illumina定制的9000个SNPs中，有8042个成功被合成至芯片；在对1450只北极熊进行基因分型后，其中5441个SNPs被证实聚类效果良好且具有多态性。利用该芯片，我们证实北极熊种群中存在快速的连锁不平衡衰减；同时在78个个体的亚样本中，相较于针对同一批个体完成基因分型的24个微卫星标记，本研究开发的SNPs能更清晰地检测到已知的遗传结构，且该结果并非由SNP筛选方案所导致。本研究报道了首批针对濒危物种开发的大规模基因分型资源之一。