Development and application of microsatellite DNA molecular markers for the laboratory red crucian carp (Carassius auratus) strain C1HD

The genetic backgrounds of crucian carp ( Carassius auratus ) and goldfish are highly similar, and these fish are often considered a single variety. It is therefore difficult to distinguish crucian carp using traditional genetic and molecular methods. In this study, we developed microsatellite markers for the laboratory red crucian carp (C1HD strain) by analyzing its genome sequence using a Perl script. We investigated the polymorphism of these potential markers in the C1HD strain, two other crucian carp lineages (DLCC strain and red crucian carp-like fish, RCC-L), and two other cyprinid species (Ryukin and koi carp, Cyprinus carpio haematopterus , KOC). Among nine screened loci, two loci (SSR-4, SSR-21) showed specific genotypes to C1HD, SSR-4, and SSR-21 observed in C1HD with 209/238 and 214/238, respectively. Additionally, one locus (SSR-763) presented one private allele in C1HD (389) and other locus (SSR-228) detected with one private allele in C1HD (135). Across the five strains, a total of 42 alleles were identified in the nine microsatellite markers. Nei’s unbiased genetic distances revealed a close relationship between the C1HD strain and the red crucian carp-like fish. The laboratory red crucian carp was recovered on an independent branch in the evolutionary tree drawn based on genetic distance. Our microsatellite makers clearly distinguish the laboratory crucian carp for RCC-L, DLCC, and Ryukin lineages.