The most commonly used nuclear markers for DNA fingerprinting
are random amplified polymorphic DNA (RAPD),
amplified fragment length polymorphism (AFLP) and micorsatellites
or short sequence repeats (SSR). Both RAPD and
AFLP markers do not require prior molecular information
whereas SSR markers require sequence information to design
primers. All these markers are widely used for analysis of
genetic diversity because of large number of loci, which can be
screened simultaneously. The differentiating power of these
markers is in the following order: SSR >AFLP > RAPD.
Both RAPD and AFLP have two alleles per locus and therefore
considered as dominant markers (presence or absence of
a band). In contrast, SSRs are able to recognize both the alleles
(co-dominant marker) and can easily differentiate between
homozygotes and heterozygotes. The application of
nuclear DNA markers in wildlife fingerprinting is summarized
in Table 2.