A Single-Laboratory Validated Method for the Generation of DNA Barcodes for the Identification of Fish for Regulatory Compliance

Abstract

The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5′ end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.

Applying COI Barcode to Identify Animal Origin of Food

“…In the iBOL system, a target gene region consisting of 648 to 655 bp starting near the 5' end of the mitochondrial cytochrome c oxidase subunit 1 was recommended for animal identification (Hebert et al, 2003). This region has been shown to reliably discriminate animals from fish (Handy et al, 2011) to mammal (Ivanova, Clare, & Borisenko, 2012). A few literature also showed that mini barcode 100 to 200 bp was more effective in obtaining DNA sequence information from specimens containing degraded DNA than full length barcode (Hajibabaei, Janzen, Burns, Hallwachs, & Hebert, 2006;Meusnier et al, 2008).…”

“…So far, several studies in the application of DNA barcoding for food detection have been reported. Handy et al (2011) reported a single-laboratory validated barcoding method for fish identification. Jones, Peters, Weland, Ivanova, and Yancy (2013) reported the use of DNA barcodes for identification of hazard animals in relation to filth in food.…”

PCR Cloning Combined With DNA Barcoding Enables Partial Identification of Fish Species in a Mixed-Species Product

“…DNA barcoding is typically used by the U.S. Food and Drug Administration (FDA) to identify fish species in food for regulatory purposes (Handy et al, 2011). In DNA full-barcoding, a ∼650 base-pair (bp) region of the cytochrome c oxidase subunit 1 (CO1) gene is sequenced and compared to reference sequences to enable species identification.…”

DNA barcoding for the species identification of commercially important fishery products in Indonesian markets

“…Seafood authentication in food control laboratories can be carried out by a number of methods that include protein-based electrophoretic and mass spectroscopy techniques (Schiefenh€ ovel & Rehbein, 2013;Wulff et al, 2013;Carrera et al, 2014) or DNAbased methods (Lockley & Bardsley, 2000;Rasmussen & Morrissey, 2008;Handy et al, 2011). Moreover, the authorities or research institutions responsible for food quality assurances are often confronted with new imported food products.…”