Plant & Animal Genomes XVI Conference

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

Testing Different Approaches For SNP-Identification In Selected Full Length cDNA Sequences From Atlantic Salmon (Salmo salar)

Rune Andreassen^{1, 2, 3} , Heidi Hagen-Larsen ¹ , Sigbjørn Lunner¹ , Bjørn Høyheim^{1, 2}

¹  Norwegian School of Veterinary Science, BasAm/Genetics, PO Box 8146 dep. 0033 Oslo, Norway.

²  CIGENE-Centre for Integrative Genetics, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway

³  Oslo University College, Faculty of Health Sciences, Oslo, Norway

SNP markers are valuable tools for a number of applications including genome analyses and relationship testing. The duplicated nature of the salmon genome as well as sequence errors might lead to a large number of false SNPs appearing as putative SNPs in EST sequences when searching for SNPs in silico. Therefore, any putative SNP needs to be further validated to make sure that it is a true single locus polymorphism.
We have obtained the full length sequence from a large number of genes by full length sequencing selected Atlantic salmon cDNA clones. Identification of SNPs in such cDNA sequences may allow these genes to be mapped, and the SNPs themselves might represent sites that affect the performance of the genes.
We have tested two strategies aiming at identifying SNPs in such cDNAs. One approach has been to manually search for putative SNPs by comparison with data in EST-databases, followed by validation of the putative SNP in a small population panel. The other approach has been to perform sequencing of the 3’UTR of the gene in individuals from a small population, aiming at detecting new SNPs at any site within the 3’UTR. A comparison of the two approaches indicates that the direct sequencing of 3’UTR might be less laborious but equally efficient when performing dedicated searches for SNPs in selected cDNA sequences. At present we have identified and validated 24 SNPs from these full length cDNA sequences, and we have started to map them onto the existing linkage map.