Development of multiplex species-specific PCR for the simultaneous identification of three closely related species in the genera Misgurnus and Paramisgurnus

Abstract

We aimed to develop a multiplex PCR method for the simultaneous detection of the three most consumed commercial loaches in East Asia: Misgurnus mizolepis, Misgurnus anguillicaudatus, and Paramisgurnus dabryanus. Phylogenetic analysis of genetic divergence and a phylogenetic tree based on the cytochrome oxidase I gene enabled successful genetic identification of the 3 species of loach. Multiplex species-specific PCR (MSS-PCR) primers designed based on single nucleotide polymorphisms were able to differentiate the species and generate PCR products among species that differed in size by at least 150 bp. The lengths of the amplified fragments were 818 bp for P. dabryanus, 669 bp for M. mizolepis, and 486 bp for M. anguillicaudatus, which could be clearly distinguished by gel electrophoresis. The three sets of PCR primers were mixed and applied to simultaneously detect the three loaches. The MSS-PCR markers designed in this study will be useful for the detection and identification of M. mizolepis, M. anguillicaudatus, and P. dabryanus.