Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp

Abstract

Thirty-six new microsatellites were identified from common carp (Cyprinus carpio L.) by screening through genes found in GenBank, EST sequences from a testis cDNA library and a genomic DNA library enriched for CA repeats. Eleven of the twenty-eight microsatellites identified from genes and ESTs were AT repeats, suggesting their high abundance in the genome of common carp. Characterization of the 36 microsatellites on a panel of 18 unrelated common carp individuals revealed that all, except two, were polymorphic with an average allele number of 7.3/locus (range: 2–15 alleles/locus). The microsatellites located in genes and ESTs showed higher allele number than those eight which were isolated from a genomic DNA library (7.7/locus vs. 4.9/locus df=32, P<0.05). Cross-species amplification showed that 41.7% (15/34) of the primer pairs from common carp amplified specific and polymorphic PCR products in the silver crucian carp (Carassius auratus gibelio). Interestingly, the success rate of cross-species amplification was lower for microsatellites located within genes and ESTs, than for those presumably located in non-coding regions. These novel microsatellites will be very useful for genome mapping and population genetic studies in both species, as well as for studying reproductive strategies of the silver crucian cap. A set of 21 polymorphic microsatellites from our study and those of others were selected as a standardized marker set to be used in studies on genetic diversity of common carp.