Development of a new SNP panel for bowhead whales (Balaena mysticetus)

Population genetic research is a critical tool for the conservation and management of marine mammals and other species.  The bowhead whale (Balaena mysticetus) is subject to aboriginal subsistence hunting in Alaska, Canada, Chukotka, and Greenland and managed by the International Whaling Commission for all those countries except Canada.  Genetic studies support conservation management plans and the determination of safe hunting quotas by providing information on levels of genetic diversity, estimates of abundance and effective population size, and stock separation.  Because bowhead populations are monitored in several countries, including genetic monitoring, there is a need for methods that can be consistently used in multiple labs that provide comparable data that can be publicly shared and built upon by successive studies.  Here we present a new panel of single nucleotide polymorphisms (SNPs), derived from multiple bowhead populations, that meet those criteria.  We describe the use of the Fluidigm SNPtype assay for analyzing 69 autosomal, 6 X-chromosome, and 1 Y-chromosome SNPs.  Results indicate that the methods herein are reliable and have low error rates.  Because SNPs are discrete sequence-based genetic markers, the panel of loci described here can be replicated, used in different labs, and are directly comparable, making SNPs more useful than existing microsatellite markers.