Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar)

validation in wild and farmed American and European populations

J. M. Yáñez, S. Naswa, M. E. López, L. Bassini, K. Correa, J. Gilbey, L. Bernatchez, A. Norris, R. Neira, J. P. Lhorente, P. S. Schnable, S. Newman, A. Mileham, N. Deeb, A. Di Genova, A. Maass

Resultado de la investigación: Article

41 Citas (Scopus)

Resumen

A considerable number of single nucleotide polymorphisms (SNPs) 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 SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs 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%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs 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.

Idioma originalEnglish
Páginas (desde-hasta)1002-1011
Número de páginas10
PublicaciónMolecular Ecology Resources
Volumen16
N.º4
DOI
EstadoPublished - 1 jul 2016

Huella dactilar

Salmo salar
single nucleotide polymorphism
Single Nucleotide Polymorphism
polymorphism
Population
genome
Salmon
Genome
salmon
Fishes
genotype
farmed fish
bioinformatics
Chile
wild fish
dissection
Genetic Association Studies
fish
North America
Computational Biology

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Citar esto

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. / Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar) : validation in wild and farmed American and European populations. En: Molecular Ecology Resources. 2016 ; Vol. 16, N.º 4. pp. 1002-1011.
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abstract = "A considerable number of single nucleotide polymorphisms (SNPs) 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 SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom({\circledR}) 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{\%}) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs 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.",
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Yáñez, JM, Naswa, S, López, ME, Bassini, L, Correa, K, Gilbey, J, Bernatchez, L, Norris, A, Neira, R, Lhorente, JP, Schnable, PS, Newman, S, Mileham, A, Deeb, N, Di Genova, A & Maass, A 2016, 'Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations', Molecular Ecology Resources, vol. 16, n.º 4, pp. 1002-1011. https://doi.org/10.1111/1755-0998.12503

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

En: Molecular Ecology Resources, Vol. 16, N.º 4, 01.07.2016, p. 1002-1011.

Resultado de la investigación: Article

TY - JOUR

T1 - Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar)

T2 - validation in wild and farmed American and European populations

AU - Yáñez, J. M.

AU - Naswa, S.

AU - López, M. E.

AU - Bassini, L.

AU - Correa, K.

AU - Gilbey, J.

AU - Bernatchez, L.

AU - Norris, A.

AU - Neira, R.

AU - Lhorente, J. P.

AU - Schnable, P. S.

AU - Newman, S.

AU - Mileham, A.

AU - Deeb, N.

AU - Di Genova, A.

AU - Maass, A.

PY - 2016/7/1

Y1 - 2016/7/1

N2 - A considerable number of single nucleotide polymorphisms (SNPs) 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 SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs 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%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs 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.

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KW - genomic selection

KW - next-generation sequencing

KW - pseudo-tetraploid

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KW - SNP array

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