Genomewide single nucleotide polymorphism discovery in Atlantic salmon ( Salmo salar): validation in wild and farmed American and European populations

• Published in: Molecular Ecology Resources
• Main Authors: Yáñez, J. M., Naswa, S., López, M. E., Bassini, L., Correa, K., Gilbey, J., Bernatchez, L., Norris, A., Neira, R., Lhorente, J. P., Schnable, P. S., Newman, S., Mileham, A., Deeb, N., Di Genova, A., Maass, A.
• Other Authors: Corporación de Fomento de la Producción, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2016
• Subjects: Atlantic salmon; Salmo salar
• Online Access: http://dx.doi.org/10.1111/1755-0998.12503; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12503; https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12503

Abstract A considerable number of single nucleotide polymorphisms ( SNP s) are required to elucidate genotype–phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNP s were identified across a set of 20 fish by whole‐genome sequencing. After applying six bioinformatic filtering steps, 200 K SNP s were selected to develop an Affymetrix Axiom ® myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNP s were validated as high quality based on clustering properties. A total of 151 509 validated SNP s showed a unique position in the genome. When comparing these SNP s against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high‐density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high‐resolution genomewide information.