Microsatellite-based genetic diversity and differentiation of foreign common carp (Cyprinus carpio) strains farmed in the Czech Republic

This study set out to improve our understanding of the molecular genetic characteristics of imported strains of common carp reared in the Czech Republic. To do this we characterized the genetic diversity and population structure of 11 carp strains including two farmed strains from Germany (Scheuerman and Glinzig mirror carp) and France (Forez and Dombez scaly carp), one farmed population from Amur river basins, and one feral population from the Ebro River (Spain), by microsatellite analysis of 10 loci. Mean heterozygosity within populations ranged from 0.584 to 0.700, and the mean number of alleles per population ranged from 5.0 to 9.8. Of the analysed loci, 92 out of 130 possible tests were found to deviate significantly (P < 0.05) from the Hardy–Weinberg equilibrium revealing significant heterozygote deficit after Bonferroni correction. Global analysis of hierarchical gene diversity (AMOVA) further revealed that the total genetic variation among populations was 21%, whilst variation within populations was estimated to be 79%. After grouping, the majority of total microsatellite loci variation appeared to be due to variation within populations. A relationship tree based on Nei's DA genetic distance and the UPGMA algorithm grouped the strains and populations into two major clusters, reflecting their affiliation to the European/Central Asian or East-Asian subspecies of common carp, rather than their country of origin. An individual assignment test (self-classification) using a Bayesian method demonstrated 89.6% accuracy in assigning individuals into their correct strains/population of origin at P < 0.05. Thus, the set of 10 highly polymorphic microsatellite markers used in the present study demonstrated significant worth in monitoring the genetic diversity of cultured common carp. Additionally, our results proved the efficiency of the conservation programme and highlighted the need for better control of genetic variability in common carp strains. This could also be useful for the conservation of carp strains in the Czech Republic.