Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Development Of 16.5K SNP-Chip For Atlantic Salmon

Matthew P Kent¹ , Ben Hayes² , Qin Xiang³ , Paul R Berg¹ , Richard A Gibbs³ , Sigbjørn Lien¹

¹  CIGENE - Centre for Integrative Genetics, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway

²  Animal Genetics and Genomics, Primary Industries Research Victoria, 475 Mickleham Rd, Attwood, Victoria, Australia 3049

³  Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

Data generated with high-throughput genotyping can be used to measure variation within and between populations, characterise genetic variation, fine map Quantitative Trait Loci (QTLs) and to improve programs by implementing Whole Genome Association (WGA) information through genome wide selection. A successful genotyping product is characterised by having a large number of evenly distributed and informative SNPs that can be robustly genotyped. We have constructed an Illumina iSelect bead-array containing probes for 16,549 Atlantic Salmon SNPs. These were assembled from three sources, (i) the alignment of EST sequences (n=9240), (ii) the resequencing and alignment to mitochondrial DNA and BAC ends (n=290), and finally (iii) Genome Complexity Reduction (GCR) was used to construct a Reduced Representation Library (RRL) representing a random selection of SNPs (n=7019). The most challenging of these three approaches (yet arguably the most attractive) is to detect SNPs through the construction of an RRL, however in the absence of a reference sequence and a larger proportion of the Atlantic Salmon genome being in a duplicated state, the identification of informative SNPs through sequence alignment poses a significant challenge. In this presentation we will describe the development of the 16.5K Salmon SNP chip and present preliminary genotyping data with a special focus on quality control and construction of a dense genetic SNP map in Atlantic salmon.