Development of amplified fragment length polymorphism (AFLP) markers suitable for genetic linkage mapping of catfish

Genomic research requires many molecular markers for construction of the genetic linkage map and for marker-assisted selection (MAS). Amplified fragment length polymorphism (AFLP) markers are inherited with Mendelian expectations in catfish and, thus, are suitable for use in gene mapping and MAS. To identify large numbers of AFLP markers, 64 primer combinations were tested to generate AFLP patterns between channel catfish Ictalurus punctatus and blue catfish I. furcatus. The 64 primer combinations amplified 7,871 bands, of which 3,081 were polymorphic between the two mating parents of channel catfish and blue catfish used to produce the reference families for mapping analysis. The primer combinations that produced fewer bands showed higher rates of polymorphism. Of the 64 primers, 53 primer combinations produced clean and reproducible AFLP profiles. Nine primer combinations produced fair AFLP profiles. The remaining two primers produced poor AFLP profiles with intensive background bands. The 53 excellent primer combinations produced 2,572 AFLP markers. These markers are suitable for use in gene and quantitative trait loci mapping of catfish by using the interspecific hybrid system. Analysis of genetic variations among strains of channel catfish indicated that AFLP should also be a valuable tool for genetic resource and population analyses in fish.