Genetic identification method for two subspecies of the indonesian short-finned eel, Anguilla bicolor, Using an allelic discrimination technique

Abstract

Background: There is an increasing pressure on tropical species of the freshwater eel genus Anguilla for use in aquaculture, so species identification methods are needed to monitor these activities and to facilitate conservation efforts. A method was developed to genetically distinguish two subspecies of the Indonesian short-finned eel, Anguilla bicolor, based on an allelic discrimination technique. Results: A single DNA nucleotide substitution in the mitochondrial DNA 16S rRNA gene was employed to identify the two subspecies where Anguilla bicolor bicolor and Anguilla bicolor pacifica possessed adenine and guanine, respectively. This substitution was highly conserved at 100% in A. bicolor bicolor (108/108) and 99.9% in A. bicolor pacifica (181/182), and the misidentification rate was estimated to be 0.34%. Subsequently, fluorescent-labeled oligo probes and PCR primers were designed and succeeded to clearly distinguish the two subspecies. Further, the other ten anguillid species that may be sympatrically distributed with A. bicolor showed negative results. Conclusions: The method developed in this study is useful to accurately identify the two subspecies of A. bicolor and can contribute to ecological studies, stock management, and conservation.