Open Access Open Badges Research article

The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

Julien Prunier1*, Betty Pelgas12, France Gagnon1, Mireille Desponts3, Nathalie Isabel2, Jean Beaulieu4 and Jean Bousquet1*

Author Affiliations

1 Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada

2 Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du PEPS CP 10380 Succ Sainte-Foy, Québec, Québec, G1V 4C7, Canada

3 Ministère des Ressources Naturelles du Québec, 880 Chemin Sainte-Foy, Québec, Québec, G1S 4X4, Canada

4 Natural Ressources Canada, Canadian Forest Service, Canadian Wood Fibre Centre, 1055 rue du PEPS CP 10380 Succ Sainte-Foy, Québec, Québec, G1V 4C7, Canada

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BMC Genomics 2013, 14:368  doi:10.1186/1471-2164-14-368

Published: 1 June 2013



The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing.


A genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years.


The sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree’s life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers.