High genetic diversity and substantial population differentiation in grass carp (Ctenopharyngodon idella) revealed by microsatellite analysis

Grass carp is one of the most important freshwater food fish species in the world. We studied genetic diversity and population relationships of grass carp by genotyping 507 individuals from nine populations using 10 polymorphic microsatellites. In five wild populations and four cultured populations, a total of 212 alleles were detected at the 10 loci. All wild and cultured populations in China showed high allelic (A = 6–13.7; Ar = 6.00–8.23) and gene diversity (Ho = 0.71–0.79 and He = 0.71–0.82), while the cultured population Cul3 located in Malaysia showed low genetic diversity (A = 6.4; Ar = 3.89, Ho = 0.48, He = 0.55). Both AMOVA and FST analysis revealed significant population structuring (FIS = 0.035, P < 0.05; FST = 0.081, P < 0.05, FIT = 0.113, P < 0.05). It is very striking that the cultured populations were significantly differentiated from wild populations, and contained high genetic diversity. The information about genetic diversity and population structure would supply a basis for future genetic improvement through selective breeding.