PAG-XVI  Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA


W24 : Aquaculture

SNP Discovery And Linkage Mapping In Atlantic Salmon

Matthew P Kent1 , Thomas Moen1,2 , Ben Hayes1,3 , Richard A Gibbs4 , George M Weinstock4 , Stig Omholt1 , Sigbjorn Lien1

1  CIGENE - Centre for Integrative Genetics, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
2  AKVAFORSK - The Institute of Aquaculture Research, Box 5010, N-1432, Ås, Norway
3  Animal Genetics and Genomics, Primary Industries Research Victoria, 475 Mickleham Rd, Attwood, Victoria, Australia 3049
4  Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

Salmon EST sequences were aligned to identify putative SNPs. After testing, we identified approximately 1000 SNPs that were non-duplicated and segregating. A subset of 309 SNPs, and 150 microsatellites, were used to develop male and female linkage maps. The length of the female map (1983 cM) is close to its expected length, whereas large variation in the length of linkage groups in the male map indicates that the true map is longer than the current map (390 cM). The sub-optimal coverage of the male map is likely related to sex-related differences in level and distribution of recombination; found here to be more extreme in Atlantic salmon than in rainbow trout. Data on linkage disequilibrium (LD) indicate that LD is increasing with decreasing distance from 10 cM and down. While the mapping described here has used relatively few markers, ongoing mapping activities require the genotyping of tens of thousands of SNPs. In collaboration with the Human Genome Sequencing Centre (Baylor College of Medicine), CIGENE is developing a strategy for Salmon SNP discovery using Genome Complexity Reduction and 454 sequencing. To date, our approach has revealed thousands of putative SNPs which will be combined with high-quality EST SNPs to produce an Illumina BeadChip for genotyping 10-60K SNPs. Data will help to improve current salmon Linkage Maps, construct Linkage Disequilibrium and QTL Maps and, in combination with physical map data, represents a portion of our contribution to the whole genome sequencing of the Atlantic salmon and Rainbow trout coordinated by the cGRASP program.