Genetic diversity of zebrafish (Danio rerio, Hamilton, 1822) in Bangladesh using DNA barcoding and RAPD techniques

Abstract

Zebrafish is one of the most important model fish species used in aquaculture research. The study of genetic diversity of wild zebrafish (Danio rerio) by RAPD markers and DNA barcoding are important tools which will help in developing commercial fish stock for the sustainable aquaculture management. The present investigation was undertaken to study the morphometric variation and genetic diversity of the zebrafish collected from 4 locations in Bangladesh (Mymensingh, Faridpur, Khulna and Munhigonj) and 12 of the samples were analyzed by RAPD marker and DNA barcoding techniques. Three random decamer primers were used for RAPD marker and two were used for DNA barcoding to amplify DNA fragments. 112 bands were scored by the primers, 22 were polymorphic. The percent polymorphic loci and gene diversity values varied within a range of 10.60–33.33 and 0.0645–1.2685 respectively. Nei’s genetic similarity between populations across all the primers ranged from 0.2812 to 1.0000. The dendrogram based on Nei’s genetic distance showed 11 clusters; the population of Faridpur was found to have maximum genetic diversity with 33.33% polymorphic loci and the Khulna population had a minimum with 10.60% polymorphic loci. Genetic diversity also found among the populations of Mymensingh and Munshigonj with 15.15% and 19.69% polymorphic loci. The clusters also revealed strong correlation with the species. For DNA barcoding, we amplified the cytochrome oxidase c subunit 1(COI) barcode sequence (680 bp long) for 4 specimens, and we compared them with reference sequences from different databases (GenBank and BOLD). Though the database is undergoing continual development, it was able to provide species matches of >99% sequence similarity for 4 samples tested. The overall sequence alignment similarity among our sampled specimens was 99.35%. Although both of the techniques are costly, recently DNA barcoding and RAPD marker has achieved support as a rapid, cost-effective and broadly applicable molecular diagnostic technique for this purpose. It can be conclude that the amplified sample used for the experiment appeared significant genetic variation among them.