SSO test for scallop forensics

The Case of the Scurrilous Scallops:
Species-Specific Oligonucleotide (SSO) test for fishery & wildlife forensics
(HD Marshall, KA Johnstone, & SM Carr (2007) Forensic Science International 167,1-7)

    The DNA sequences of the same gene vary within species as well as among species. Within-species variation can be the basis of genetic disease, for example when a DNA mutation alters the structure of a key protein, as in cystic fibrosis. A routine test for such mutations uses so-called allele-specific oligonucleotides (ASOs), which are short pieces of single-stranded DNA ("oligos") that stick selectively to the particular gene sequence ("alleles") of interest. The presence or absence of the disease-causing allele can thus be detected directly. Genetic differences between species arise as a result of evolution, and these differences can be detected by means of species-specific oligonucleotides (SSOs). Two species that are difficult to distinguish by their appearance (for example, codfish and pollock) can be readily distinguished by their DNA sequence differences

    The DNA sequence of a gene called CoxI is known to differ between two species of scallops found in the Northwest Atlantic, Sea Scallops and Icelandic Scallops. The SSO test shown here combines an oligo for a gene region identical in both species with two primers specific for regions of the DNA sequence that differ between species. The size of the DNA fragment to which the oligos stick identifies the species: Sea Scallops are expected to have a larger fragment (932 - 313 = 619bp), versus a shorter fragment (932 - 473 = 459bp) in Icelandic Scallops.

    In the forensic application, a fisherman had in his hold a load of scallops which he claimed were from the open fishery for Icelandic scallops, but which enforcement officers suspected included some fraction from the closed fishery for Sea scallops. Because a small proportion of bycatch 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 tested in this experiment, eight (blue arrows) show the smaller DNA fragment and 72 the larger fragment, which indicates that 90% are Sea Scallops. In the complete series of more than 900 scallops from two vessels, nearly two-thirds were Sea Scallops. This led to conviction and fine (St. John's Telegram, March 3rd, 2007). The multiplex SSO test provides a rapid, direct means of forensic identification of large population sample series, and can be adapted to other species.