Identification of single nucleotide polymorphisms for use in a genetic stock identification system for greater white-fronted goose (Anser albifrons) subspecies wintering in California

Abstract

California provides wintering habitat for most greater white-fronted geese ( Anser albifrons [GWFG]) in the Pacific Flyway and this population has rapidly increased since the 1980s. Increased harvest of GWFG wintering in California may prevent agricultural depredation while providing increased hunting opportunities. However, changes in harvest levels are unlikely to be uniform across the species because of the presence of multiple subspecies of GWFG in the Pacific Flyway, each with their own population distribution and trends. White-fronted geese in the Cook Inlet Basin of south-central Alaska, a potentially vulnerable subspecies (Tule goose, A. a. elgasi ), are among the geese that winter predominantly in the Sacramento Valley and Suisun and Napa marshes of north-central California. Efforts to limit sport harvest of Tule geese are complicated because although the subspecies is phenotypically larger and darker in color than other subspecies, they can be difficult to identify in the field and in hunter bag checks. To assist in an accurate assessment of Tule goose harvest, we used double-digest restriction site-associated deoxyribonucleic acid sequencing (ddRAD-seq) techniques to develop a genetic stock identification panel of single nucleotide polymorphisms (SNPs) to differentiate Tule geese from individuals belonging to other GWFG subspecies and populations that winter in California. Although the panel we developed was designed and tested for Fluidigm SNP-type technology, the ddRAD-seq sequences can be used to design SNP panels for use in other platforms.