DEVELOPMENT OF POLYMORPHIC EST MARKERS SUITABLE FOR GENETIC LINKAGE MAPPING OF CATFISH

The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquaculture, Auburn University, Auburn, AL 36849 USA

Expressed sequence tag (EST) markers are important for gene mapping and for marker-assisted selection (MAS). To develop EST markers for use in catfish gene mapping, 100 randomly picked cDNAs from the channel catfish (Ictalurus punctatus) pituitary library were sequenced. The EST sequences were used to design PCR primers to amplify channel catfish and blue catfish (I. furcatus) genomic DNAs. PCR products of the ESTs were analyzed to determine length polymorphism between the channel catfish and blue catfish. Eleven polymorphic EST markers were identified. Five of the 11 EST markers were from known genes and the other six from unidentified ESTs. The polymorphic EST markers will be useful for genetic linkage mapping of catfish. The low rate of polymorphism of EST even in the interspecific hybrid system of channel catfish and blue catfish provides strong demands for establishing radiation hybrid panels of channel catfish. Most EST sequences would be mapped if the radiation hybrid panels are available. Seven ESTs were found to be associated with microsatellite sequences. This association would make mapping of these loci more likely because of high polymorphic rates of microsatellites. Using the codons generated from this EST analysis and those from the GenBank, codon analysis was conducted for channel catfish. Analysis of channel catfish gene sequences indicated highly biased codon usage, with 16 codons being preferably used. These codons were more preferably used in highly expressed ribosomal protein genes and in highly expressed pituitary hormone genes. G/C-rich codons are less used in channel catfish than those in other vertebrates suggesting AT-richness of the channel catfish genome.