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Using the DCode System to Identify DNA Sequence Variation for Studies of Population Structure in Marine Organisms

ot be ideal (particularly for fragments without a GC-clamp), many polymorphisms will still be detected. This fall-back option is useful in cases where the size of the PCR product is not known in advance, as in the case of some introns.

Population biologists searching for intraspecific polymorphisms are drawn to introns, which often show a greater degree of site and size variation than coding regions. Introns may be amplified using conserved primers targeted to flanking exon sequence, a strategy termed exon-primed intron-crossing (EPIC) amplification.7 When the size of a homologous intron varies among species, one may analyze the smaller products by direct gradient gel electrophoresis, and use a RFLP/DGGE approach for the larger ones.

This two-pronged approach may be used in developing polymorphic markers when available universal primers are inadequate. Using available cDNA sequence data, one may design primers to amplify a moderate-sized (100400 bp) product with a suitable melting profile for DGGE. If the resulting PCR product is larger than expected due to the presence of an intron, it can still be screened for polymorphisms with the RFLP/DGGE approach.

Both population genetics surveys and genetic mapping require numerous polymorphic DNA markers. Denaturing gel electrophoresis, in its various forms, offers a flexible and powerful means of identifying polymorphisms, as well as screening large population samples for identified variants.


References
1. The Simple Fools Guide to PCR, 2nd ed. (Palumbi, S. et al.) Special Publ., Dept. of Zoology, University of Hawaii, Honolulu (1991).

2. Molecular Markers, Natural History and Evolution (Avise, J. C.) Chapman an
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