Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River

• Published in: Molecular ecology resources Vol. 11; no. s1; pp. 20 - 30
• Main Authors: CAMPBELL, NATHAN R, NARUM, SHAWN R
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01-03-2011; Wiley Subscription Services, Inc
• Subjects: Animals; coho; Consensus Sequence; DNA Primers; Expressed Sequence Tags; Freshwater; Genotype; Northwestern United States; Oncorhynchus kisutch; Oncorhynchus kisutch - genetics; Oncorhynchus mykiss; Oncorhynchus nerka; Oncorhynchus tshawytscha; Polymorphism, Single Nucleotide; Rivers; Salmon - genetics; Sequence Analysis, DNA; single-nucleotide polymorphism; sockeye; Taqman; Northwestern United States; USA, Columbia R
• ISSN: 1755-0998; 1755-098X; 1755-0998
• DOI: 10.1111/j.1755-0998.2011.02977.x

Single-nucleotide polymorphisms (SNPs) have potential for broad application in population and conservation genetics, but availability of these markers is limited in many nonmodel species. In this study, genomic and expressed sequence tagged (EST) sequences from closely related salmonids (Chinook salmon and rainbow trout) were used to design primers for amplification and sequencing of sockeye (Oncorhynchus nerka) and coho (Oncorhynchus kisutch) salmon DNA for SNP discovery. One hundred and six primer sets were designed and tested for amplification in each species. An ascertainment panel of 32 diverse individuals from each species was used as template for PCR amplification and Sanger sequencing. In total, 21 647 bases of consensus sequence were screened in sockeye salmon and 20 784 bases in coho salmon with 93 and 149 SNP sites identified, respectively. Sixty-four SNP sites were chosen for assay development, and 54 of the assays were validated by comparison with genotype and sequence data (O. nerka = 23; O. kisutch = 31). These validated SNP assays along with 142 other available SNP assays [O. nerka = 103 (126 total); O. kisutch = 30 (61 total)] were used to genotype collections of O. nerka (N = 5) and O. kisutch (N = 4) from various sites in the Columbia River to evaluate the utility of these markers in this region. Results from factorial correspondence analysis indicate that these SNP markers are capable of distinguishing O. nerka populations, but O. kisutch collections were less distinct because of their common ancestry.