Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners

Authors

  • Nathalie Pavy,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    Search for more papers by this author
    • These authors contributed equally to this work.
  • France Gagnon,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    Search for more papers by this author
    • These authors contributed equally to this work.
  • Philippe Rigault,

    1. Gydle Inc., Québec, Canada, QC
    Search for more papers by this author
    • These authors contributed equally to this work.
  • Sylvie Blais,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    Search for more papers by this author
  • Astrid Deschênes,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    Search for more papers by this author
  • Brian Boyle,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    Search for more papers by this author
  • Betty Pelgas,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada, QC
    Search for more papers by this author
  • Marie Deslauriers,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Natural Resources Canada, Canadian Wood Fibre Centre, Québec, Canada, QC
    Search for more papers by this author
  • Sébastien Clément,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Natural Resources Canada, Canadian Wood Fibre Centre, Québec, Canada, QC
    Search for more papers by this author
  • Patricia Lavigne,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada, QC
    Search for more papers by this author
  • Manuel Lamothe,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada, QC
    Search for more papers by this author
  • Janice E.K. Cooke,

    1. Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, Canada, AB
    Search for more papers by this author
  • Juan P. Jaramillo-Correa,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, México, D.F., Mexico
    Search for more papers by this author
  • Jean Beaulieu,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Natural Resources Canada, Canadian Wood Fibre Centre, Québec, Canada, QC
    Search for more papers by this author
  • Nathalie Isabel,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    2. Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Canada, QC
    Search for more papers by this author
  • John Mackay,

    1. Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    Search for more papers by this author
  • Jean Bousquet

    Corresponding author
    • Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada, QC
    Search for more papers by this author

Correspondence: Jean Bousquet, Fax: 418-656-3493;

E-mail: jean.bousquet@sbf.ulaval.ca

Abstract

High-density SNP genotyping arrays can be designed for any species given sufficient sequence information of high quality. Two high-density SNP arrays relying on the Infinium iSelect technology (Illumina) were designed for use in the conifer white spruce (Picea glauca). One array contained 7338 segregating SNPs representative of 2814 genes of various molecular functional classes for main uses in genetic association and population genetics studies. The other one contained 9559 segregating SNPs representative of 9543 genes for main uses in population genetics, linkage mapping of the genome and genomic prediction. The SNPs assayed were discovered from various sources of gene resequencing data. SNPs predicted from high-quality sequences derived from genomic DNA reached a genotyping success rate of 64.7%. Nonsingleton in silico SNPs (i.e. a sequence polymorphism present in at least two reads) predicted from expressed sequenced tags obtained with the Roche 454 technology and Illumina GAII analyser resulted in a similar genotyping success rate of 71.6% when the deepest alignment was used and the most favourable SNP probe per gene was selected. A variable proportion of these SNPs was shared by other nordic and subtropical spruce species from North America and Europe. The number of shared SNPs was inversely proportional to phylogenetic divergence and standing genetic variation in the recipient species, but positively related to allele frequency in P. glauca natural populations. These validated SNP resources should open up new avenues for population genetics and comparative genetic mapping at a genomic scale in spruce species.

Ancillary