Development of a Genotyping-in-Thousand By Sequencing (GT-seq) Panel for Traceability in Chilean Blue Mussel

Genomics technology allows development of thousands of SNP markers in non-model species in a fast and affordable way. However, genotyping thousands of SNPs is unnecessary for many studies, and can be difficult, time consuming and expensive if only a small panel of markers is necessary to address research questions. GT- seq is a method for amplicon sequencing a relatively small number of SNP in many samples based in NGS technology. Here we developed a GT-seq panel of 90 SNPs for Mytilus chilensis and tested it in 576 samples of M. chilensis, M. galloprovincialis, M. edulis, M. trossulus, and mixed populations collected in Chile, California, Canada, China, Falkland Islands, Poland, and Spain. Initially 153 SNPs were evaluated for inclusion in the GT- seq panel. By evaluating results of a test plate, we selected loci with high genotyping rates (>75%) and concordance (>75%) with a previous genotyping method (Sequenon® or RAD-seq). Missing genotypes from RAD-seq data were the cause of most of the discrepancies between methods as opposed to discordant genotypes. The final GT-seq panel included 16 EST-SNPs and 74 RAD-SNPs. These SNPs were tested for species identification, assignment of individuals to geographical origin (only in Chilean samples), and temporal stability of allele frequencies in two Chilean populations. For species identification, 46 loci were included in the panel differentiating M. chilensis from other mussels. Also promising results were obtained in testing geographical origin with the 90 SNP panel, but more SNPs are necessary to improve accuracy for fine scale applications of traceability. Grants FONDECYT 1130302 & FONDEF ID16I10013