Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased in size, rates of litter production and average litter size have also decreased, while cub mortality and average time to independence have increased. Although these changes have potential evolutionary consequences, little is yet known about the adaptive genetic variation in body size or fat accumulation that would have to underlie any such change. In this study, we used high-throughput Illumina sequencing to develop SNPs from pooled blood and fat transcriptomes, using samples from five adult female polar bears and five (unrelated) dependent cubs. In total, we generated 371,258 transcripts of which 36,755 were deemed to be “full length” (i.e., covered more than 90% of their best BLAST hit), and we identified 63,020 SNPs. Since this study was conducted, we have used a subset of these SNPs to develop an Illumina BeadArray for quantitative genetics research in Western Hudson Bay.

Custom Perl script for extracting SNPsPerl program used to extract SNPs. Properly accounts for REFSKIP characters (i.e., "<" and ">") that result from spliced alignments and seemed to be problematic in more widely available SNP calling packages, such as samtools and varscan.getsnpsfrommpileup.plSNP VCF fileVCF file containing info for SNPs called using the getsnpsfrommpileup.pl script. Settings used were: coverage >= 10, freq. of minor allele >= 0.2, read support for minor allele >= 3, number of alleles = 2. All SNPs were also verified using the program SysCall, and were retained only if the posterior probability of being a variant was >= 0.95.pb_syscallsnps.vcf.txtContig annotation filePutative gene and gene ontology annotations for transcripts that were deemed to be "full length" (i.e., cover >= 90% of their best blastx hit in RefSeq). These sequences are available on NCBI under the BioProject accession PRJNA193538.annotations.annot