A first generation BAC-based physical map of the channel catfish genome

A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF) of 46,548 Bacterial Artificial Chromosomes (BAC) clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1) anchoring 19 of the largest contigs to the microsatellite linkage map 2) comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP) patterns seen in Southern blots, and 3) contig sequencing.This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits.Channel catfish production is now the leading aquaculture species in the U.S., with 600 millions pounds processed annually [1]. Consequently, selective breeding of catfish broodstock is ongoing in order to improve the genetic potential of the species for commercial production. To support selective breeding research, molecular tools are being developed to help researchers characterize the catfish genome, which consists of 28 pairs of autosomes and one pair of sex chromosomes, and identify genomic regions that control important production traits. However, a considerable amount of available data has not been organized within the structural framework of catfish chromosomes. Briefly, framework genetic linkage maps have been produced based on microsatellite loci [2] and Amplified Fragment Length Polymorphism (AFLP) loci [3]. Channel catfish Expressed Sequence Tags (EST) have been identified from several tissues [4,5] and clustered and annotated in the Gene Index Project [6