Molecular identification of species and ploidy of Carassius fishes in Lake Biwa, using mtDNA and microsatellite multiplex PCRs

We established an efficient and reliable method to identify the species and ploidy of Carassius fishes in Lake Biwa (C. cuvieri, C. buergeri, and the latter’s polyploid) using a combination of multiplex mitochondrial DNA haplotype-specific PCR and ploidy determination based on nuclear DNA microsatellite PCR. The high accuracy of ploidy determination was confirmed by flow cytometry. This method can also identify triploid clonal lines and provide information about their genetic diversity and structure. The method is applicable to ecological and evolutionary studies of Carassius fishes in Lake Biwa throughout their entire life history.