Genetic diversity of common carp (Cyprinus carpio L.) strains breed in Poland based on microsatellite, AFLP, and mtDNA genotype data

Abstract The common carp ( Cyprinus carpio L.) has a long-standing history in Polish pond aquaculture, which has given rise to a great number of local breeds, strains and hatchery populations. They are well adapted to their local conditions, play an important role for fisherman's livelihood s and embody valuable genetics for future breeding programs. Proper maintenance of animal genetic resources (AnGR) requires an appropriate strategy based upon the precise knowledge of their genetic structure. This study genetically characterizes 20 common carp strains breed in Poland alongside with wild carp from Onuma Lake in Japan. We study three different types of genetic markers including the 963 AFLP markers, a set of 11 microsatellite loci (STR) and DNA sequences of the mitochondrial control region (D-loop). Bayesian clustering analysis of microsatellite loci divided the studied strains into 17 distinct clusters. Using population assignment test 92.4% of carp individuals were correctly assigned to their strain of origin. Microsatellite and AFLP marker analysis have shown the moderate but significant level of genetic variation between strains (AMOVA 23% and 18.2% respectively). AFLP and STR analysis of genetic distances gave equivalent values and were positively correlated with high values of the Mantel test ( r  = 0.553, n  = 20, p  = 0.001). Only two mtDNA haplotypes (H5 and H2) were detected in all studied carp strains with H2 being the most prevalent. This is the first comprehensive genetic research of common carp strains breed in Poland which provided crucial data for the national conservation strategy. This study means that this resource can now be placed within the context of similar studies worldwide allowing the further improvement and breeding work.