Characterization, polymorphism assessment, and database construction for microsatellites from BAC end sequences of channel catfish (Ictalurus punctatus): A resource for integration of linkage and physical maps

To apply genome-based technologies for genetic improvements using marker-assisted selection, genome research involving genetic linkage mapping and physical mapping is required, and integration of genetic and linkage maps would significantly enhance the capacities for genome research. In catfish, the major aquaculture species in the United States, linkage and physical maps have been constructed. However, integration of genetic linkage and physical maps demands large-scale, genome-wide hybridizations, or genetic mapping of polymorphic markers derived from bacterial artificial chromosome (BAC) clones whose locations are known from the physical map. In this work, we identified a large number of microsatellites from BAC end sequences of channel catfish, characterized the microsatellites, tested their utility for linkage mapping in a resource family used for genetic mapping, and constructed a web-searchable database for BAC end sequences, their linked microsatellites, microsatellite primers, PCR conditions, and polymorphic information. A total of 3652 microsatellites in 2744 distinct BACs were identified. Of these, 1100 had sufficient and complex flanking sequences for PCR primer design. We have tested 500 primer pairs and found 211 (42.2%) were polymorphic and segregating in the resource family used for genetic mapping. These microsatellites represent a major fraction of co-dominant polymorphic markers identified to date in catfish, and should be a valuable resource for genetic mapping to increase linkage map resolution, and for integration of genetic linkage and physical maps.