Project Leaders:
William Davidson, Ben Koop

Lead Institutions:
Simon Fraser University, University of Victoria

Research Funding Program:
Competition I

Technology Applications:
Salmon microarrays, broodstock analysis, biomarkers for fish health, vaccine development

Project Website:
Genomic Research on Atlantic Salmon Project

The overall goal of the salmon genome program is to co-ordinate all aspects of genomic research on Atlantic salmon and to use this information to improve salmonid resources. Atlantic salmon is the species of choice for this genomics project, in part because of its economic importance but also because of its fundamental scientific interest. More than 80% of the farmed salmon in BC are Atlantic salmon, which has become the industry standard worldwide and its production is only expected to increase. Understanding its genome and biology will allow better breeding programs using marker-assisted selection procedures.

This project will amalgamate the linkage map, the physical map, and the chromosomes for the Atlantic salmon. Genetic linkage maps based on many markers were constructed for several species but most relied on RAPDs or AFLPs and were of limited use across families. Recently, low-resolution genetic maps with microsatellite markers were constructed for salmonids. Researchers plan to create one complete resource by co-ordinating the physical and theoretical genetic maps.

Salmon, trout, and charr (salmonids) are descended from a common ancestor that underwent a genome duplication event 25 – 100 million years ago. Therefore, instead of the regular two copies of chromosomes, the salmonid genome had four copies of each chromosome. Over time, duplicated set of chromosomes accumulate mutations and diverge from each other so comparing the salmonids will provide clues to the tempo and mode of genomic evolution.

The third goal of GRASP is to determine how Atlantic salmon combat pathogens. Researchers will analyze gene expression and protein level changes of the immune system components. The knowledge will assist in designing vaccines and breeding programs to select for decreased susceptibility.

In the initial phase, the researchers developed a microarray to measure gene expression levels in salmonids that is a valuable tool for many researchers. The knowledge and tools from this project will help understand the interaction between this commercially important, scientifically interesting organism and its environment.

Project Publications:
von Schalburg, K.R., McCarthy, S.P., Rise, M.L., Huston, J.C., Davidson, W.S. & Koop, B.F. (2006). Expression of morphogenic genes in mature ovarian and testicular tissues: Potential stem-cell niche markers and patterning factors. Molecular Reproduction and Development, 73(2), 142-152.

Artieri, C.G., Mitchell, L.A., Ng, S.H.S., Parisotto, S.E., Danzmann, R.G., Hoyheim, B., Phillips, R.B., Morasch, M., Koop, B.F. & Davidson, W.S. (2006). Identification of the sex-determining locus of Atlantic salmon (Salmo salar) on chromosome 2. Cytogenetic and Genome Research, 112(1-2), 152-159.

Morrison, R.N., Cooper, G.A., Koop, B.F., Rise, M.L., Bridle, A.R., Adams, M.B. & Nowack, B.F. (2006). Transcriptome profiling of the gills of amoebic gill disease (AGD)- affected Atlantic salmon (Salmo salar L.): A role for tumor suppressor protein p53 in AGD pathogenesis? Physiological Genomics, 26: 15-34.

Danzmann, R.G., Cairney, M., Davidson, Ferguson, M.M., Gharbi, K., Guyomard, R., Holm, L.-E., Leder, E., Okamoto, N., Ozaki, A., Rexroad III, C.E., Sakamoto, T., Taggart, J.B. & Woram, R.A. (2005). A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae). Genome, 48(6), 1037-1051.

Rise, M.L., Douglas, S.E., Sakhrani, D., Williams, J., Ewart, K.V., Rise, M., Davidson, W.S., Koop, B.F. & Devlin, R.H. (in press). Multiple microarray platforms utilized for hepatic gene expression profiling of growth hormone transgenic coho salmon with and without ration restriction. Journal of Molecular Endocrinology.

von Schalburg, K.R., Rise, M.L., Brown, G.D., Davidson, W.S. & Koop, B.F. (2005). A comprehensive survey of the genes involved in maturation and development of the rainbow trout ovary. Biology of Reproduction, 72(3), 687-699. Epub Oct 20, 2004.

Thorsen, J., Zhu, B., Frengen, E., Osoegawa, K., de Jong, P.J., Koop, B.F., Davidson, W.S. & Høyheim, B. (2005). A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics, 6(1), 50.

Ng, S.H.S., Artieri, C.G., Bosdet, I.E., Chiu, R., Danzmann, R.G., Davidson, W.S., Ferguson, M.M., Fjell, C.D., Hoyheim, B., Jones, S.J.M., et al. (2005). A physical map of the genome of Atlantic salmon, Salmo salar. Genomics, 86(4), 396-404.

von Schalburg, K.R., Rise, M.L., Cooper, G.A., Brown, G.D., Gibbs, A.R., Nelson, C.C., Davidson, W.S., Koop, B.F. (2005). Fish and Chips: Various methodologies validate and demonstrate utility of a 16,006-gene salmonid microarray. BMC Genomics 6,126.

Hunt, P.N.D., Wilson, M.D., von Schalburg, K.R., Davidson, W.S. & Koop, B.F. (2005). Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein. BMC Genomics 6,165.

Rise, M.L., von Schalburg, K., Brown, G.D., Devlin, R.H., Mawer, M.A., Kuipers, N., Busby, M., Beetz-Sargent, M., Alberto, R., Gibbs, V., Hunt, P., Shukin, R., Zeznik, V., Nelson, C., Jones, S.R.M., Smailus, D., Jones, S., Schein, J., Marra, M., Davidson, W.S. & Koop, B.F. (2004). Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Research 14(3), 478-49.

McKay, S.J., Trautner, J., Smith, M.J. , Koop, B.F. & Devlin, R.H.. (2004). Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes. Genome, 47(4), 714-723.

Woram, R.A., McGowan, C., Stout, J.A., Gharbi, K., Ferguson, M.M., Hoyheim, B., Davidson, E.A., Davidson, W.S., Rexroad, C. & Danzmann, R.G. (2004). A genetic map for Arctic charr (Salvelinus alpinus): evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents. Genome, 47(2), 304-315.

Rise, M.L., Jones, S.R.M., Brown, G.D., von Schalburg, K.R., Davidson, W.S., Koop B.F. (2004). Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. Physiological Genomics, 20(1), 21-35.

Woram, R.A., Gharbi, K., Sakamoto, T., Hoyheim, B., Holm, L.-E., Naish, McGowan, C., Ferguson, M.M., Phillips, R.B., Stein, J., Guyomard, R., Cairney, M., Taggart, J., Powell, R., Davidson, W.S. & Danzmann, R.G. (2003). Comparative genome analysis of the primary sex-determining locus in salmonid fishes. Genome Research, 13(2), 272-280.

Rexroad III, C.E., Lee, Y., Keele, J.W., Karamycheva, S., Brown, G., Koop, B.F., Gahr, S.A., Palti, Y. & Quackenbush, J. (2003). Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenetics & Genomics Research 102(1-4), 347-354.