GT-seq panel development
To identify potential SNPs for our GT-seq panel, we screened 411,094 SNP
loci identified from ddRADseq data generated from 327 polar bears in
Jensen et al. (2020). We filtered this dataset to retain loci that were
successfully genotyped in ≥ 85% of individuals and had a minor allele
frequency of at least 0.25. Retained loci were thinned to one SNP per
50,000 bp using the polar bear reference genome (GenBank
GCA_000687225.1; Liu et al., 2014) to reduce possibility of linkage.
These filters resulted in 442 SNP loci being retained (See Table
S1 for full filtering workflow). To allow for sex identification, we
added two SNPs previously recognized as sex-linked in polar bears (Pagès
et al., 2009). We validated our GT-seq panel of 442 SNPs and designed
primers as described in Supplemental Information: GT-seq Panel
Development and Validation .