Using DNA 'barcodes' to combat fish fraud



Snapper fillets



Now that Memorial Day has passed, we tend to do a lot more grilling here in the Dark Lab.  The weather here in SoCal falls into a predictable perfection and any given evening is perfect for throwing something on the grill.  So, I head out to my local grocery store and look for a nice fish… snapper maybe?  Looking at the package, it’s definitely a fish but is it really snapper?  I can’t tell.  In fact, studies show that up to 70% of fish sold as snapper is actually something else.  The FDA tries to monitor fish but they are probably more focused on safety rather than accuracy.  However, there has been a lot of press lately about mislabeling of fish.  Last week, the New York Times ran an article (link) with some shocking statistics about how frequently fish are mislabeled.  According to a report by the non-profit group Oceana (2.3 Mb pdf here), for every three packs of fish you buy, one of them will be wrong. 

Oceana references a number of scientific studies, including a paper by Wong and Hanner (abstract), who use a PCR-based approach to analyze the DNA sequences of fish in the marketplace.  They found that some substitutions are obvious fraud.  For example, fish labeled as red snapper (sold at $3 per pound) was actually redfish (that would cost 72 cents a pound).  Fish labeled as white tuna sushi was actually tilapia.  These are flagrant mistakes, and it is not at all clear whether this is done on purpose or is the product of the complex network of processors and middle-men that are required to bring a fish out of the sea and to your dinner plate.  However, some mistakes are less apparent… for example, Atlantic halibut was labeled as Pacific halibut.  No big deal, right?  What if you knew that Atlantic halibut was endangered?  Would you still buy it? This type of mislabeling suggests some fishermen may be catching more than their quota of threatened or endangered fish and packaging them as something else.  Another recent article goes into more detail about the social and financial implications of fish fraud (abstract).

Want to know what fish you are buying?  It’s a great DIYbio project.  If your hackerspace has the ability to do DNA sequencing (or you can send sequencing samples via the hack shack) then checking your fish can be pretty easy.  You will probably want to sequence several spots in the genome and will need sequencing primers for each (which are cheap and easy to design).  Once you have the DNA sequence from your fish, you can use an online tool called Blast (link) to search the genome database for your sequence and it will tell you what species it is from.  If you already know the sequence (from the primer design, for example), then you can simply align the correct sequence with your fish’s DNA and see if you get a perfect match.  This method will give you a pretty good idea if you have the right fish as long as there are differences in the DNA sequence between the various species.  Sometimes, they can be very similar.

If you have access to a hackerspace with a PCR machine (and the reagents!) and a way to run an agarose (DNA) gel, there are several other options.  You can do an AFLP analysis, which is a very sensitive way to look for polymorphisms (changes) in DNA.  A recent paper by Maldini (abstract) outlines the approach and applies it to identifying fish.  They claim that even closely related fish can be identified.  Another PCR-based option is to amplify a gene using a species-specific primer.  In this case, you see good amplification (ie, a band on a gel) only when the DNA of that species is present.  Two advantages with the PCR approach are that you don’t need much DNA and it doesn’t need to be all that pure (both are big advantages for the biohacker). One thing you will need is a set of PCR primers for the species of fish you are buying.  I hope that someday these will also be readily available in any decent hackerspace, but until then, you will have to get them yourself.  The Wong and Hammer paper has some primers listed and primers for key genes from the most common types of market fish are freely available on the internet.  If they can’t be found directly, you can also design them from the fish’s genome.  Genbank (link) has some of this information but another good source is the website for the Fish Barcode of Life (link).  This great organization is trying to catalog all fish, including those we eat.  Eventually, they will have links to the genome of every fish so you can use that for primer design.  As an added DIYbio bonus, they are also looking for additional data from people like YOU!  Not with the DNA sequencing, but with the development of range maps that indicate where the different species of fish are found.  This is a great opportunity for all you fishermen out there (go here to see how you can report a sighting).  It’s also a way for biopunks to make important contributions to this effort while doing a little home-based food surveillance. 

So, did you notice?  The snapper picture is mislabeled... it's actually tilapia. At least you didn't pay 10 bucks for this blog post.