A magnetic bead-based DNA extraction protocol suitable for high-throughput genotyping in shrimp breeding programs

Tan, Cheryl K.Y., Cowley, Jeff A., and Jerry, Dean R. (2019) A magnetic bead-based DNA extraction protocol suitable for high-throughput genotyping in shrimp breeding programs. Genetics of Aquatic Organisms, 3 (2). pp. 47-56.

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Abstract

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 KingFisher™ 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.

Item ID: 61446
Item Type: Article (Research - C1)
ISSN: 2587-2265
Keywords: shrimp, prawn, DNA extraction, magnetic bead, high-throughput,genetic analysis
Additional Information:

This article is available Open Access via the publisher's website.

Funders: ARC Industrial Transformation Research Program
Projects and Grants: IH130200013
Date Deposited: 01 Mar 2020 19:31
FoR Codes: 07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070401 Aquaculture @ 50%
07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070405 Fish Physiology and Genetics @ 50%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830101 Aquaculture Crustaceans (excl. Rock Lobster and Prawns) @ 100%
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