Random amplified polymorphic DNA markers: Usefulness for gene mapping and analysis of genetic variation of catfish

Catfish are the most important aquacultural species in the United States. A genetic linkage map is needed to improve efficiency of breeding by marker-assisted selection (MAS), and for identification, isolation and eventual cloning of commercially important genes. To identify DNA-based genetic polymorphism for constructing a genetic linkage map of catfish, we tested 100 random amplification of polymorphic DNA (RAPD) primers for their utility in identifying genetic polymorphism in catfish. The overall polymorphism was low among strains within a species for both channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). However, considerably higher levels of polymorphism were detected between channel catfish and blue catfish. Among the 100 primers tested, 42 produced highly clean and reproducible RAPD profiles; 33 produced medium quality RAPD profiles; and 25 produced poorly reproducible RAPD profiles or non-polymorphic RAPD profiles. The 75 high and medium quality primers generated 462 polymorphic bands, an average of 6.1 bands per primer. The RAPD markers were highly reproducible in a size range from 200 to 1500 base pairs (bp). They were transmitted to F₁ hybrids as dominant markers. There was no difference in RAPD profiles between channel catfish x blue catfish F₁ hybrids or their reciprocal hybrids. The markers segregated in F₂ or backcross progeny with ratios as expected from Mendelian inheritance.