Amplified Fragment Length Polymorphism (AFLP) fingerprinting was used to detect genetic
variability in two stocks of common carps (Majalaya carp and Sinyonya carp) and second
generation gynogens derived from the Majalaya carp. Primer combinations, E-AAC/M-CAA, EAGG/
M-CAC and E-ACC/M-CTT yielded 299 selectively amplified loci of which 66.2% were
polymorphic. Maximum polymorphism was evident in the Majalaya carp and minimum among
the gynogens. Four types of AFLP bands which were useful to differentiate the stocks in question
were identified. Band Sharing Index (BSI) matrix was generated from the band binary
value sets. Maximum average BSI was exhibited by the gynogens and minimum by the
Majalaya carp. Inter-stock comparisons showed the gynogens to be closest to the Majalaya and
farthest from the Sinyonya stock
