Expansion of the genomics research on Atlantic salmon Salmo salar L. project (GRASP) microarray tools K. R. VON SCHALBURG*, G. A. COOPER*, J. LEONG*, A. ROBB*, R. LIEPH*, M. L. RISE†, W. S. DAVIDSON‡ AND B. F. KOOP*§ *Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, †Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and ‡Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada Salmonids are the most widely studied group of fish, and in the last few years, genomics technologies have begun to contribute to this rich biology. The first salmonid microarrays appeared in 2004 and since then several dozen studies have demonstrated the utility of genomic approaches. The widespread use of the genomics research on Atlantic salmon project 16 k array and greatly expanded genome resources have led to the development of an experimental 5 k oligo (70-mer) array and a 32 k cDNA microarray in the near future. In this paper, the authors examined some of the procedures used in the development of past arrays and reexamined them in light of new genomic data available. Some preliminary control experiments of the new 5 k array were investigated that examine oligo designs based on distance from the polyA tail, the effects of mismatches and cross-species hybridization specificity. Beneficial approaches are also identified in the development of the new 32 k cDNA array. # 2008 The Authors Journal compilation # 2008 The Fisheries Society of the British Isles Key words: contig; cDNA; EST; GRASP; microarrays; salmonid. INTRODUCTION The Salmonidae family includes whitefish and ciscos (subfamily Coregoninae); graylings (Thymallinae); trout, salmon and charr (Salmoninae). Salmonids belong to the Protacanthopterygii (smelts, pikes and salmon) group, which has been separated from the other highly studied euteleost lineages of Ostario- physi (zebrafishes, catfishes, flathead minnows, etc.) c. 217 million years ago (MYA) and from the Acanthopterygii (cods, cichlids, fugus, sticklebacks and rockfishes) c. 290 MYA (Ishiguro et al., 2003; Ramsden et al., 2003; Steinke et al., 2006). Salmonids have been classified into nine genera and roughly 68 species (Nelson, 1994). Considerable basic biological knowledge of trout and salmon has been developed as a result of their widespread use in scientific research, as an environmental sentinel species and their use as a food and sport fish. More is known about the physiology and biology of salmonids than any §Author to whom correspondence should be addressed at present address: Department of Biology, University of Victoria, P. O. Box 3020, Victoria, British Columbia, V8W 3N5 Canada. Tel.: (250) 472 4071; fax: (250) 472 4075; email: bkoop@uvic.ca Journal of Fish Biology (2008) 72, 2051–2070 doi:10.1111/j.1095-8649.2008.01910.x, available online at http://www.blackwell-synergy.com 2051 # 2008 The Authors Journal compilation # 2008 The Fisheries Society of the British Isles