The fluorogenic ribonuclease protection (FRIP) assay was used to detect single nucleotide polymorphisms (SNPs) in commercially produced fish products. By using fluorescence resonance energy transfer (FRET) between fluorophore and quencher labeled probes, the species-specific cleavage of sample RNA was detected by measuring the fluorescence intensity during the FRIP assay. We were able to discriminate raw and thermally processed eel and tuna species using the FRIP-based SNP detection method. Furthermore, the intensity of fluorescence was correlated with the mutant/wild-type ratio. These results suggest that the FRIP assay is a useful method for the in situ confirmation of labels of fishery foods during food production.
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