PCR-RFLP analysis of mitochondrial DNA to differentiate populations of climbing perch (Anabas testudineus) in Thailand

Abstract

Climbing perch (Anabas testudineus) is a common tropical fresh- and brackish water fish species in Asia. Its aquaculture has received attention in many Asian countries both as an emerging economic species and affordable protein source. The Thai Department of Fisheries, therefore, has been interested in a selective breeding program for this species. However, the lack of genetic data prevents such systematic breeding program. We performed polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of mitochondrial D-loop region to differentiate six wild and two hatchery populations of Anabas testudineus in Thailand (n = 21 - 29). Analysis of variance indicated that hatchery populations had lower genetic diversity than wild populations (P = 0.01; average haplotype diversity = 0.52 and 0.10 in the wild and hatchery samples, respectively). However, there was no clear relationship between the presence of haplotypes and geographic locations. Almost all populations were genetically distinct. Analysis of Molecular Variance (AMOVA) indicated 57.83% among population genetic variation. Pairwise FST values showed significant divergence in almost all population pairs, except for two pairs (two hatchery samples; and Chonburi, CH and Ratchaburi, RT). Neighbor-Joining dendrogram based on Nei’s genetic distance suggested high divergence between Sakhon Nakhon, SN and the remaining samples, but it did not resolve the relationships among Nakhon Pathom (NP), RT, CH and Nakhon Si Thammarat (NS) representing major river systems in Thailand. The PCR-RFLP of the mitochondrial D-loop region was an effective technique to evaluate genetic diversity within and among populations. However, the level of polymorphism may not be adequate to resolve the relationships among some populations. The results can aid the management of existing genetic variation within hatcheries and the development of a base population for selective breeding.