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Add To Calendar 20/02/2017 14:30:0020/02/2017 14:50:00America/ChicagoAquaculture America 2017DEVELOPMENT OF A high throughout single nucleotide polymorphism assay FOR GENETIC MONITORING OF RED SNAPPER aquaculture and stock enhancement   Room 11The World Aquaculture Societyjohnc@was.orgfalseanrl65yqlzh3g1q0dme13067DD/MM/YYYY

DEVELOPMENT OF A high throughout single nucleotide polymorphism assay FOR GENETIC MONITORING OF RED SNAPPER aquaculture and stock enhancement  

Adrienne Norrell, America Fujimoto, Jason Stannard, Eric A. Saillant*,

 The University of Southern Mississippi, School of Ocean Science and Technology, Thad  Cochran Marine Aquaculture Center, Ocean Springs, MS, USA


The red snapper, Lutjanus campechanus, supports major commercial and recreational fisheries in the southern United States. Aquaculture of the species is being developed in the context of a pilot program in Mississippi to evaluate the feasibility of large scale production of juveniles for stock enhancement or grow out to commercial size. A genetic program in support of the aquaculture project is in progress and aims to assist with the management of captive breeding and the monitoring of genetic impacts of releases. Genomic resources including a draft genome sequence and a high-density linkage map were previously developed and applied to study red snapper population structure using a Restriction site Associated DNA (RAD) sequencing approach. The objective of this work was to develop an efficient high throughput assay for a subset of the Single Nucleotide Polymorphisms (SNPs) discovered and characterized during linkage mapping and population genomic analysis in order to monitor captive and wild populations during breeding and stock enhancement.

Candidate SNPs and associated flanking sequences were evaluated in silico to determine suitability for incorporation on a Fluidigm® dynamic array (D3 Assay Design) and an initial set of 96 SNP Type assays were synthesized and used to screen a panel of 95 DNA samples representing red snapper geographic locations. The tested panel included 48 putatively neutral SNPs selected based on their position on the red snapper linkage map; one SNP was selected on each end of each of the 24 linkage groups to generate a panel of 48 loci expected to segregate independently. The remaining SNPs included loci showing a possible signature of divergent selection during an initial RAD-sequencing survey of red snapper geographic populations and markers expected to distinguish southern and northern red snapper. Pre-amplified DNA, and SNP Type assays, were assayed on an Integrated Fluidic Circuit (IFC) that accommodates 96 assays by 95 samples. Thirty-four of the 96 initial assays were rejected due to poor quality data, assay failure, monomorphism, or high disagreement with the RAD-sequencing genotypes. Another 49 assays were designed and evaluated to replace failing initial assays and produce the final panel of 96 SNPs. The overall agreement between the final Fluidigm and RAD sequencing datasets was 94.31%. A total of 486 red snapper of various ages collected from 5 geographic populations in US waters were genotyped at the 96 SNPs. The analysis of neutral loci revealed no significant genetic variance among geographic populations (ΦCT = - 0.001, P = 0.745) or among year class within region (P = 0.406). Selected loci revealed a small but significant variance among regions (ΦCT = 0.008, P = 0.001) but no variance among year class within region (P = 0.805).

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