consortium Genomics Research on All Salmon
 
Executive Summary
The consortium for Genomics Research on All Salmon Project (cGRASP) is a Genome Canada funded project in the category of fisheries; one of the five areas identified as having strategic importance for this country and one in which we can be a world leader. 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 and worldwide it has become the industry standard. Atlantic salmon production is ranked among the seven largest yielding fish species in the world and its production is expected to increase in the coming years.
cGRASP will provide an opportunity for aquaculture to harness the power of genomics. Genetic maps, or specifically the genetic markers that comprise the map, are an essential resource for the genetic analysis of quantitative traits (QTLs) of aquaculture interest. The genetic mapping of a commercially important species increases the efficiency of breeding programs through the use of marker-assisted selection procedures. Selective breeding programs and genetics will play an increasingly important role in achieving improvements in the performance of salmon broodstock. Future expansion of the aquaculture industry is anticipated to occur primarily through gains in productivity. Traits that may be amenable to genetic improvement include growth rate, delayed maturity, flesh quality, pigment uptake, temperature tolerance, and disease resistance.
The overall aim of cGRASP is to coordinate all aspects of genomics research on Atlantic salmon. However, it is important to note that genomic information gained from Atlantic salmon will be applicable to other salmonids including Pacific salmon (e.g rainbow trout) and Arctic char; species that are commercially important in their own right. The information gained from cGRASP will:
  1. assist conservation and enhancement of wild populations,
  2. benefit commercial harvesting through the identification of specific stocks,
  3. help maintain the lucrative sports fisheries,
  4. enable fundamental scientific questions concerning the evolution of salmonid genomes to be answered, and
  5. facilitate monitoring the expression of genes and proteins in a wide variety of natural and altered environments for regulatory agencies.
cGRASP has three major scientific goals:
  1. to tie together the linkage map with the physical map;
  2. to locate genes of known function on the physical map and to understand how a duplicated genome reorganizes itself and controls sex-determination; and
  3. to examine gene expression at the transcriptional level and the translational level in several tissues and to identify molecules induced by physiological responses to stress, acclimatization, pathogens, and exposure to natural and introduced chemicals. Twelve specific objectives (see section IV for details) were proposed to Genome Canada and these were approved without revisions.
Progress during the first 3 years of GRASP has been excellent. The project is on schedule or slightly ahead of schedule.
A BAC library, comprising 313,000 clones with an average insert size of 190,000 base pairs, has been constructed from DNA from a male Atlantic salmon. 200,000 BACs have been HindIII fingerprinted producing ~4200contigs (~80% of the clones). The preparation of high quality cDNA libraries and the sequencing of many different transcripts therein, represented a key objective of cGRASP. Over 100 cDNA libraries were constructed from a variety of tissues and developmental stages. More than 100,000 reads of the 3' ends of these expressed sequence tags (ESTs) have been completed resulting in over 40,000 contigs or genes. The data show that:
  1. ~30% of new reads still result in novel sequences;
  2. ~25% of new contig sequences show similarity to data in the Gene Ontology database;
  3. there are an estimated 9000 polymorphisms in the database; and
  4. the rainbow trout sequences (3'-UTR) are 90-97% similar to their Atlantic salmon counterparts.
cGRASPs expertise in collating and analyzing EST data has been recognized by the international salmonid community and groups from the USA, France, Norway as well as from within Canada have provided EST data for inclusion in cGRASPs salmonid database. The success of producing a wide variety of cDNA libraries and obtaining so many independent sequences enabled the development of a microarray. Inserts from 16,000 cDNAs were PCR amplified, purified, quantified, and spotted on glass slides. The microarray provides excellent sensitivity and general applicability for all salmonids. We have demonstrated novel proofs of utility in three major areas; health (disease and treatment), environmental assessment and conservation biology.
The results of cGRASP are presented at genomics and fisheries conferences and in invited seminars. The cGRASP International Workshop attracted many fish physiologists, salmonid biologists, and environmental scientists allowing GRASP to develop a large number of collaborations in Canada and abroad with academic institutions, research facilities, government laboratories, and industry. This has allowed us to engage the broader salmonid research community.
GRASP has already established itself as a leader in salmonid genomics and Canada, through GRASP, is now recognized as a major player internationally in aquaculture-related genomics.