Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD) markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822) in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001) departure from homogeneity and the F ST values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA) dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.

The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna), two estuarine (Kuakata and Sundarbans) and one marine (Cox's Bazar) populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant F ST values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters.

Characterization of different strains of common carp (Cyprinus carpio L.) using molecular markers is essential for the management of this fish in respect to the evaluation of the potential genetic effects induced by hatchery operations and the genetic improvement of carp varieties. Five microsatellite loci (MFW1, MFW2, MFW11, MFW15 and MFW20) were analyzed for the molecular characterization of four common carp strains, i.e. scaled carp, mirror carp, red carp and koi carp. We observed differences in heterozygosities and the average numbers of alleles but not in polymorphic loci (P95) among the strains. Koi carp displayed the highest level of variability in terms of heterozygosity. The Nm values and the F ST values indicated a low level of gene flow and high level of differentiation among the strains. The highest genetic distance was observed between the scaled carp and the koi carp whilst the lowest genetic distance was found between the red- and koi carp. The unweighted pair group method with averages (UPGMA) dendrogram resulted in two clusters, one containing only the scaled carp and the other the remaining three varieties. Microsatellite markers have been found to be effective tools for characterization of different strains of common carp.