Design of a 9K illumina BeadChip for polar bears ( Ursus maritimus) from RAD and transcriptome sequencing

• Published in: Molecular Ecology Resources
• Main Authors: Malenfant, René M., Coltman, David W., Davis, Corey S.
• Other Authors: Environment Canada, World Wildlife Fund, Natural Sciences and Engineering Research Council of Canada
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2014
• Subjects: Hudson; Hudson Bay; Ursus maritimus
• Online Access: http://dx.doi.org/10.1111/1755-0998.12327; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12327; https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12327

Abstract Single‐nucleotide polymorphisms ( SNP s) 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 SNP s are needed to equal the resolution of a single microsatellite, and reliable large‐scale genotyping of SNP s remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears ( U rsus 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 SNP s and 3000 transcriptomic SNP s were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNP s ordered from Illumina, 8042 were successfully printed, and – after genotyping 1450 polar bears – 5441 of these SNP s 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 SNP s 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.