Developing Single Nucleotide Polymorphisms for Identification of Cod Products by RAD-Seq

Animals : an Open Access Journal From MDPI
Shoujia JiangXinxin You

Abstract

The increase in the rate of seafood fraud, particularly in the expensive fishes, forces us to verify the identity of marine products. Meanwhile, the definition of cod lacks consistency at the international level, as few standards and effective application methods are capable of accurately detecting cod species. Genetic fingerprinting is important for both certifying authenticity and traceability of fish species. In this study, we developed a method that combines DNA barcoding and the restriction-site associated DNA sequencing (RAD-Seq) approach for the identification of cod products. We first obtained 6941 high-quality single nucleotide polymorphism (SNP)s from 65.6 gigabases (Gb) of RAD-Seq raw data, and two sequences that contain SNPs were finally used to successfully identify three different cod product species, which are Atlantic cod (Gadusmorhua), Greenland turbot (Reinhardtiushippoglossoides), and Patagonian toothfish (Dissostichuseleginoides). This SNP-based method will help us to identify the products, which are sold under the name of "Xue Yu" (Cod) in China, and works in parallel with existing fish identification techniques to establish an efficient framework to detect and prevent fraud at all points of the seafood sup...Continue Reading

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Datasets Mentioned

BETA
LC146707.1

Methods Mentioned

BETA
genotyping
RAD-Seq
PCR
Assay
PCRs
amplicon sequencing
electrophoresis

Software Mentioned

Cstacks
SOAPnuke
Ustacks
MEGA7
Primer3
BLAST
Primer
BLASTn
Sstacks

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