Scallop SSO test

Species-Specific Oligonucleotides (SSOs) as a forensic DNA test
[HD Marshall, KA Johnstone, & SM Carr (2007) Forensic Sci Int'l, 167, 1-7]

    The concept of allele-specific oligonucleotides (ASOs) can be extended to species-specific oligonucleotides (SSOs). The DNA sequences of the Cytochrome Oxidase I gene are known for many species of scallops, including two found in the Northwest Atlantic, Sea Scallops (Placopecten magellanicus) and Icelandic Scallops (Chlamys icelandica). The multiplex test shown here combines an anchor primer for a DNA sequence identical in both species (ScallopR2) at position 932 with primers specific for either species (PmaCOIF1 and CisCOIF2), which are differentiated at positions 313 and 473, respectively. The PCR amplification product from Placopecten is thus expected to be 932 - 313 =  619bp in length, versus a shorter 932 - 473 = 459bp in Chlamys. That is, the size of the fragment indicates species identity directly.

    In "The Case of the Scurrilous Scallops", a fisherman had a load of scallops that he claimed were from the open fishery for Icelandic scallops (Chlamys). Enforcement officers suspected they were instead from the closed fishery for Sea scallops (Placopecten). Since a small proportion of by-catch from the closed fishery might be considered acceptable, the legal question was: What fraction of the total catch was from the prohibited species? DNA was extracted from individual scallops and amplified in the multiplex SSO test with the three primers. Of the 80 scallops in the test above, all but eight (blue arrows) show the larger DNA fragment, which indicates that 90% are Placopecten.  In the complete series of more than 900 scallops from two vessels, almost two-thirds were Placopecten. This resulted in conviction and fine.

    The multiplex SSO test provides a rapid, direct means of forensic identification of large population sample series, without the necessity of secondary DNA sequencing, RFLP mapping, or fingerprinting, and can be adapted to other loci and species.

All text material ©2016 by Steven M. Carr