Utility of Single Stranded Conformation Polymorphism (SSCP) method to identify two related freshwater prawn species

Abstract

Freshwater culture prawn industry is mainly based on Macrobrachium rosenbergii (De Man) inmany countries. However, now there is a growing interest in many Asian countries to use Macrobrachium malcolmsonii (Milne Edwards) as a potential candidate in aquaculture programs due to its high growth rate. In Sri Lanka too, freshwater prawn culture is mainly based on M. rosenbergii. However, there is a possibility to use M. macolmsonii in future in aquaculture programs, as the presence of this species is reported from the eastern part of Sri Lanka. Although, the adults of two species show a few morphological differences, the appearance of young individuals of both species are identical. Therefore, in many occasions identification and separation of the above two species is a troublesome task. The delineation of species levels using reliable and cost effective methods is an important point in effective management programs in aquaculture. This preliminary study was designed to determine the utility of Single Stranded Confirmation Polymorphism (SSCP) method to delineate two economically important freshwater prawn species, M. rosenbergii and M. malcolmsonii in Sri Lanka. Partially amplified mitochondrial 16S rRNA gene region was sequenced for both species and the number of nucleotide differences was estimated. The sequence length of the both DNA fragments were approximately 430-440 bp and the difference between two sequences was approximately 19bp. A cost effective molecular marker; SSCP technique was carried out using the same PCR product to determine the utility of this technique in delineation of above two species. However, the SSCP technique failed to construct the proper secondary structures and unable to differentiate DNA fragments derived from the two species. This may be due to the formation of more stable and similar secondary structures.

The possibility of using more variable gene regions in the identification of M. rosenbergii and M. malcolmsonii species using SSCP method is suggested.