High Throughput SNP Genotyping of White Sturgeon: A Polyploid Species in Conservation and Aquaculture

Genotyping in thousands by sequencing (GT-seq) is a high throughput and cost effective technique for genotyping thousands of individual samples at several hundred loci using Illumina sequencing. This method was originally developed for genotyping diploid organisms but the stability of allele specific signal using this technique make it amenable for genotyping organisms of higher ploidy levels. Specifically, primers are designed such that neither allele is preferentially amplified and a sufficient amount of DNA is interrogated that the relative counts for each allele reflect genomic copy number. Still, accurate determination of nine different genotypic categories for any given SNP locus in the reportedly octoploid White sturgeon genome was a significant obstacle. During initial testing of GT-seq in this organism, SNP loci clustered into five categories rather than nine, simplifying genotyping and suggesting a tetraploid rather than octoploid genome structure. Here we describe the development of a panel of primers suitable for targeted SNP genotyping by GT-seq in White sturgeon (Acipenser transmontanus). We also present a modified GT-seq genotyping pipeline for use with polyploid organisms.