Development of polymorphic EST markers suitable for genetic linkage mapping of catfish

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 complementary DNAs from the channel catf ish (Ictalurus punctatus) pituitary library were sequenced. The EST sequenc es were used to design primers to amplify channel catfish and blue catfish (I. furcatus) genomic DNAs. Polymerase chain reaction 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 t he 11 EST markers were from known genes and the other six were from unident ified ESTs. Seven ESTs were found to be associated with microsatellite sequ ences. Analysis of channel catfish gene sequences indicated highly biased c odon usage, with 16 codons being preferably used. These codons were more pr eferably used in highly expressed ribosomal protein genes and in highly exp ressed pituitary hormone genes. G/C-rich codons are less used in channel ca tfish than those in other vertebrates suggesting AT-richness of the channel catfish genome.