Genetic diversity of wild zebrafish Danio rerio populations available in Bangladesh

Abstract

The morphometric and genetic variations of 4 wild populations of zebrafish ( Danio rerio ) in Bangladesh were studied using DNA barcoding and RAPD (Random Amplified Polymorphic DNA). The zebrafish populations were as ZMS (zebrafish from the Brahmaputra river, Mymensingh), ZFP (zebrafish from the Kumar river, Faridpur), ZKH (zebrafish from the Moyurriver, Khulna) and ZMG (zebrafish from the Aarial Beel, Munshiganj). The morphometric variations were insignificant to establish the genetic structure and diversity of these populations. Therefore, the genetic variation was analyzed with DNA barcoding and RAPD techniques. FishF1 and FishR1 primers were used for barcoding with amplification of Cytochrome Oxidase C subunit 1(COI) gene region and OPA03, OPA04 and OPF01 primers were used for RAPD analysis. In DNA barcoding analysis, the database provided species matches of 100% sequence similarity for these 4 wild fish populations with D. rerio . The overall sequence alignment similarity among these populations was 99.40%. The neighbor-joining phylogenetic tree was constructed from these COI barcode sequences also revealed genetic relationships and diversity among these populations. In RAPD analysis, a total number of 112 bands were found where 22 bands were polymorphic, indicated 19.64% polymorphism among these 4 wild populations. The percent polymorphic loci and genetic distance varied within a range of 14.00–26.67 and 0.2877–1.6094 respectively. Nei's genetic similarity among these 4 populations across all the primers ranged from 0.2000 to 0.7500. The Dendrogram based on Nei's genetic distance showed 3 clusters indicating the ZFP population is the maximum genetically diversified among them however; the ZMS and ZKH populations were in the same cluster. The knowledge of the molecular variation of wild zebrafish could be helpful for planning more effective and efficient managing strategies for this model species and also provide a significant contribution to zebrafish research all over the world.