Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing

• Published in: BMC Genomics
• Main Authors: Fridjonsson, Olafur, Olafsson, Kristinn, Tompsett, Scott, Bjornsdottir, Snaedis, Consuegra, Sonia, Knox, David, de Leaniz, Carlos Garcia, Magnusdottir, Steinunn, Olafsdottir, Gudbjorg, Verspoor, Eric, Hjorleifsdottir, Sigridur
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2011
• Subjects: Atlantic salmon; North Atlantic; Salmo salar
• Online Access: https://pure.uhi.ac.uk/en/publications/9475298d-7536-448e-84d8-b424b4dec118; https://doi.org/10.1186/1471-2164-12-179

Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon (Salmo salar) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual.