Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

Abstract

Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing approximately 89 kb we observed a frequency of 4.30 x 10(-3) SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.

A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single‐Nucleotide Polymorphisms

“…Variation was analyzed at 72 nuclear and 1 mitochondrial SNP with the primer and probe sequences outlined by Smith et al (2005aSmith et al ( , 2005bSmith et al ( , 2005cSmith et al ( , 2007, Miller et al (2008). A listing of all the SNPs surveyed is given in Table 2.…”

“…The benefits of using SNPs were suggested to be ease of data standardization among laboratories, high throughput, high among-population diversity, lower genotyping errors, and lower cost of analysis per individual (Smith et al 2005b(Smith et al , 2005d. However, there was no consensus among agency laboratories as to the preferred technique to use for GSI in Chinook salmon.…”

“…The repeatability of genotyping was evaluated by repeat PCR analysis and scoring of the genotypes of individual fish. Discrepancies in scoring were observed in 8 of the 15,360 genotypes scored across all loci, for a genotyping error rate of 0.05%.Variation was analyzed at 72 nuclear and 1 mitochondrial SNP with the primer and probe sequences outlined by Smith et al (2005a, 2005b, 2005c. A listing of all the SNPs surveyed is given in Table 2.…”

Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment

“…The data for 45 SNP loci included three mitochondrial and 42 nuclear loci described in Elfstrom et al (2006) and Habicht et al (2010). Chinook salmon data were drawn from Seeb et al (2009); data for 52 SNPs included one mitochondrial and 51 nuclear loci (Smith et al 2005a(Smith et al , b, 2007Narum et al 2008). All collections were obtained between 2004 and 2009 (Table 1).…”

Genomics and Genome Sequencing: Benefits for Finfish Aquaculture

“…There have been several attempts to identify SNPs in individual genes in Atlantic salmon (Ryynanen & Primmer, 2006) and other salmonids (Smith et al, 2005), but these were smallscale efforts. It was not until large EST databases became available that an intensive search was undertaken for SNPs that could be tied to actual genes .…”