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标记具有诸多优势，包括可更精准地估算种群参数、更精细地解析种群结构，以及对数量性状开展更精确的基因组剖析。不过，要达到单个微卫星标记的分辨率，需要使用大量单核苷酸多态性标记，且在非模式生物中实现可靠的大规模单核苷酸多态性基因分型仍是一项挑战。本研究开发了一款9K规格的Illumina Infinium 微珠芯片（Illumina Infinium BeadChip）用于北极熊（Ursus maritimus）的基因分型，该芯片将用于两项研究：(i) 加拿大北极熊种群的精细种群结构解析；(ii) 西哈德逊湾亚群表型性状的基因组架构分析。为此，研究人员对环北极分布范围内的38头北极熊开展了限制性酶切位点相关DNA（restriction-site associated DNA, RAD）测序，并对来自西哈德逊湾的10个个体进行了血液/脂肪转录组测序。研究人员分别主要基于基因组间距与基因功能，筛选出6000个RAD测序衍生的单核苷酸多态性标记与3000个转录组单核苷酸多态性标记用于该芯片。从Illumina定制的9000个单核苷酸多态性标记中，最终成功合成8042个；在对1450头北极熊进行基因分型后，其中5441个标记被证实聚类效果良好且具有多态性。利用该芯片，研究团队揭示了北极熊种群中快速的连锁不平衡衰减现象；同时在78个个体的亚样本中证实，相较于为同一批个体分型的24个微卫星标记，本研究开发的单核苷酸多态性标记能更清晰地检测出已知的遗传结构，且该结果并非由单核苷酸多态性的筛选策略所驱动。本研究报道了首批针对受威胁物种开发的大规模基因分型资源之一。