Genetic diversity of common carp in Vietnam using direct sequencing and SSCP analysis of the mitochondrial DNA control region

The aquaculture of common carp (Cyprinus carpio L.) in Vietnam is based upon both indigenous and introduced stocks which have not been subject to study using modern molecular genetic methods to any significant extent. Twenty strains or populations of common carp in Vietnam represented by 968 fish were screened for variation in mitochondrial control region fragments using a combination of direct DNA sequencing and Single Strand Confirmation Polymorphism (SSCP) analysis. Common carp samples from China, Japan, Indonesia, and Hungary were analysed for comparison. Sequencing revealed that Vietnamese common carp have high haplotype, but low nucleotide diversity and represent a mixture of indigenous and introduced strains. The SSCP procedure resolved eight haplotypes that distinguished Indonesian, Hungarian and Vietnamese strains and which varied significantly among hatchery and wild Vietnamese common carp populations. Intra-population diversity was least in experimental common carp lines, maintained at the Research Institute for Aquaculture No 1 and greatest within hatchery stocks. Relationships among populations based on SSCP haplotype frequencies showed that the RIA1 Vietnamese white common carp strain is closely related to wild populations, which in turn are closely related to six of the eleven hatchery stocks. The other five hatchery stocks had higher levels of interpopulation variation and mostly showed a closer relationship to Indonesian yellow carp strains. The Hungarian carp strain was highly divergent from all other populations suggesting that this strain has not contributed significantly to the establishment of cultured stocks in Vietnam, based on this maternally inherited marker. The SSCP procedure shows considerable potential for rapid genotyping and genetic characterization of common carp and therefore, for investigation of diversity in wild stocks and broodstock management.