Genotyping-In-Thousands (GTseq) Genetic Marker Design for Four Aquatic Species

The Department of Fisheries and Oceans (DFO) has a requirement to develop, design and test 500 GTseq markers that will produce repeatable that can be used in genetic analyses related to management of aquatic species in Canada. The work will involve the following: To obtain a contract to develop, design and test 500 GTseq markers that will produce repeatable genotypes that can be used in genetic analyses related to management of aquatic species in Canada. To meet this objective, we would like to develop panels for four different species. Two of these species, Beluga (Delphinapterus leucas) and Inconnu (Stenodus leucichthys) have been identified as requiring this resource for management and two additional species that will be identified. Recent advances in next-generation sequencing (NGS) technology have provided methods to increase the proportion of the genome analyzed and allow neutral and adaptive diversity to be assessed. Once important regions of the genome are identified, it is possible to develop sets of single nucleotide polymorphisms (SNPs) through genotyping-in-thousands by sequencing (GTseq). With this method, many SNPs can be sequenced simultaneously by using multiplexed PCR primers in a consistent and reproducible manner. Therefore, the design, testing, and validation of GTseq genetic markers will ensure genotyping capabilities are available to researchers and will provide high quality genomic data to the Arctic and Ontario & Prairie regions to support Fisheries & Ocean’s mission to promote economically prosperous maritime sectors and fisheries, and sustainable aquatic ecosystems. Design, testing, and validation of 500 GTseq genetic markers to conduct genetic studies on up to four different aquatic species. GTseq genetic markers Must be designed for genotyping samples on an Illumina MiSeq. The Contractor will also provide support, as needed, to assist in further optimizing laboratory and data analysis set up for genotyping the developed markers in the genetics and genomics laboratory at the Freshwater Institute. The Freshwater Institute will provide the Contractor genomic data and DNA suitable for marker testing and validation.