Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Integration Of The Genetic And Physical Maps And The Karyotype Of Atlantic Salmon (Salmo salar)

Krzysztof P. Lubieniecki¹ , Jay W. Park¹ , Siemon H. S. Ng¹ , Jonathan Tang¹ , Keith A. Boroevich¹ , Roy G. Danzmann² , Ruth B. Philips³ , Ben F. Koop⁴ , William S. Ddavidson¹

¹  Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.

²  Department of Zoology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

³  School of Biological Sciences, Washington State University, Vancouver, Washington, 98686-9600, USA.

⁴  Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada.

As part of the Consortium for Genomic Research on All Salmonids Project (cGRASP) and as a foundation for sequencing the Atlantic salmon genome, we are integrating the genetic map and the physical map and linking them to the chromosomes in this species. Two BAC libraries were constructed using an EcoRI or Sau3AI partial digest of DNA from the same Norwegian male, and 226,050 clones have been fingerprinted using HindIII. This has resulted in a physical map that comprises 4,338 contigs containing two or more clones and 34,206 singletons. The SALMAP consortium developed male and female linkage maps using two families from the River Tweed in Scotland. These maps were based primarily on anonymous (Type II) microsatellite markers. In order to expand the genetic maps and to make them more informative for comparative genomics, we have data-mined the Atlantic salmon EST databases for Type I microsatellites and identified 2,035 such markers. To date approximately 100 ESTs have been mapped on to the SALMAP genetic maps. In addition, we examined BAC-end sequences for microsatellites and found 1,067 that could be used to join the genetic and physical maps. Approximately 120 BAC contigs have been positioned on to the linkage maps so far. BACs that contain mapped microsatellite loci have been used to match linkage groups with chromosomes using fluorescent in situ hybridiazation. The data from the physical map, the linkage maps and the karyotype and their integration can be seen at the following website: grasp.mbb.sfu.ca.