From Germs to Mammals in Aqua
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Genetics of Aquatic Organisms 2019, Vol 3, Num, 2     (Pages: 47-56)

A Magnetic Bead-Based DNA Extraction Protocol Suitable for High-Throughput Genotyping in Shrimp Breeding Programs

Cheryl K.Y. Tan 1-2 ,Jeff A. Cowley 1-3 ,Dean R. Jerry 1-2-4

1 Australian Research Council (ARC) Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD 4811, Australia
2 Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
3 Aquaculture, CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
4 Tropical Futures Institute, James Cook University Singapore, Singapore
DOI : 10.4194/2459-1831-v3_2_02 Viewed : 4795 - Downloaded : 8921 Due to their convenience, magnetic bead-based nucleic acid extraction kits are commonly used in shrimp genotyping and pathogen screening applications. However, in advanced breeding programs requiring the testing of many thousands of shrimp, their cost can be prohibitive. Various permutations of different Proteinase K digestion, tissue lysis and bead washing buffers as well as magnetic bead types were thus evaluated to devise a high-throughput shrimp DNA extraction (SDE) protocol capable of recovering high-purity DNA using a KingFisherTM Flex Magnetic Particle processor. When genotyped using a MassARRAY® platform (Agena Bioscience) requiring 60-61 genome regions to be co-amplified in a single multiplexed PCR, DNA extracted from shrimp muscle tissue using either the SDE protocol or a commercial kit generated comparable single-nucleotide polymorphism (SNP) call data. The SDE protocol also extracted high-purity DNA from salmon fin clips. It thus offers potential to markedly reduce the costs of large-scale genotyping in shrimp and salmon breeding programs. Keywords : Shrimp, Prawn, DNA extraction method, Magnetic bead, High-throughput, Genetic analysis