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 mtDNACytochrome Oxidase I gene are
known for many species of scallops, including two in the Northwest
Atlantic: Sea Scallops (Placopecten
magellanicus) and Icelandic Scallops (Chlamys icelandica). The
multiplex PCR 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 = 619bpin
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).
Enforcement
officers might consider a
small proportion of by-catch from the closed fishery permissible.
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. It has been adapted to other loci and species.