Development of Single Nucleotide Polymorphism (SNP) Markers for Rapid, Inexpensive, and Standardized Identification of Pallid (Scaphirhynchus albus) and Shovelnose (S. platorynchus) Sturgeon Larvae

The purpose of this project was to develop inexpensive, standardized, and high throughput Single Nucleotide Polymorphism (SNP) markers that discriminate between pallid (Scaphirhynchus albus) and shovelnose (S. platorynchus) sturgeon for use as a larval identification tool. A total of 67 polymorphic sites was identified in DNA sequences from three genes: Recombination Activating Gene-1, Beta Actin, and Beta-2-Microglobulin. Allele frequencies from the 10 most variable SNPs were characterized for both pallid and shovelnose sturgeon in three geographically separated populations throughout the range of the pallid sturgeon. To create a standardized method of genotyping SNPs for larval pallid and shovelnose sturgeon, 5\u27 nuclease allelic discrimination (TaqMan) assays were designed for two unlinked SNPs that exhibited the greatest allele frequency differences between species. A power analysis compared these SNP loci and their diagnostic power for species discrimination compared to sixteen microsatellite loci currently used for species discrimination (Schrey et al. 2007) One SNP locus was the most powerful marker for species identification in the upper and middle Missouri River. This study provides practical genetic tools for species discrimination between pallid and shovelnose that will facilitate understanding addressing questions that were previously too costly, labor intensive or technically challenging to answer