A first generation BAC-based physical map of the channel catfish genome.
BACKGROUND
Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL) and the effective positional cloning of genes.


RESULTS
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.


CONCLUSIONS
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.
Quiniou
Sylvie M-A
SM
USDA-ARS/CGRU, 141 Experiment Station Rd, Stoneville, MS 38776, USA. squiniou@ars.usda.gov
Waldbieser
Geoffrey C
GC
Duke
Mary V
MV
D000818:Animals; D001483:Base Sequence; D015139:Blotting, Southern; D022202:Chromosomes, Artificial, Bacterial; D017931:DNA Primers; D019075:Electrophoresis, Capillary; D008040:Genetic Linkage; D016678:Genome; D007059:Ictaluridae / Q000235:genetics*; D020161:Physical Chromosome Mapping; D012150:Polymorphism, Restriction Fragment Length; D040641:Quantitative Trait Loci
D017931:DNA Primers