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United States Department of Agriculture

Agricultural Research Service

Research Project: CATFISH GENETICS, BREEDING, AND PHYSIOLOGY Title: A First Generation Bac-Based Physical Map of the Channel Catfish Genome

Authors
item Quiniou, Sylvie
item Waldbieser, Geoffrey
item Duke, Mary

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 6, 2007
Publication Date: February 6, 2007
Citation: Quiniou, S.M., Waldbieser, G.C., Duke, M.V. A first generation bac-based physical map of the channel catfish genome. Biomed Central (BMC) Genomics.

Interpretive Summary: Quite an amount of genetic data is now available for catfish. However, that data has not yet been organized in the context of the chromosomes. Bacterial artificial chromosome (BAC) clones containing each a fragment of the catfish genome have been produced which all together cover the catfish genome many times over. A genome-wide physical map was recently constructed from more than 46,548 BAC clones organizing those clones into 1,782 clusters. This will provide us with exact location of gene of interest in the genome.

Technical Abstract: 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. The resulting assembly can be accessed at http://www.ars.usda.gov/Main/docs.htm?docid=14234.

Last Modified: 11/27/2014
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