Publications (4)10.15 Total impact
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Article: Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners.
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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.Molecular Ecology Resources 01/2013; · 3.06 Impact Factor -
Article: Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression.
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ABSTRACT: Marker-assisted selection holds promise for highly influencing tree breeding, especially for wood traits, by considerably reducing breeding cycles and increasing selection accuracy. In this study, we used a candidate gene approach to test for associations between 944 single-nucleotide polymorphism markers from 549 candidate genes and 25 wood quality traits in white spruce. A mixed-linear model approach, including a weak but nonsignificant population structure, was implemented for each marker-trait combination. Relatedness among individuals was controlled using a kinship matrix estimated either from the known half-sib structure or from the markers. Both additive and dominance effect models were tested. Between 8 and 21 single-nucleotide polymorphisms (SNPs) were found to be significantly associated (P ≤ 0.01) with each of earlywood, latewood, or total wood traits. After controlling for multiple testing (Q ≤ 0.10), 13 SNPs were still significant across as many genes belonging to different families, each accounting for between 3 and 5% of the phenotypic variance in 10 wood characters. Transcript accumulation was determined for genes containing SNPs associated with these traits. Significantly different transcript levels (P ≤ 0.05) were found among the SNP genotypes of a 1-aminocyclopropane-1-carboxylate oxidase, a β-tonoplast intrinsic protein, and a long-chain acyl-CoA synthetase 9. These results should contribute toward the development of efficient marker-assisted selection in an economically important tree species.Genetics 03/2011; 188(1):197-214. · 4.01 Impact Factor -
Article: Evidence for low genetic diversity and metapopulation structure in Canada yew (Taxus canadensis): considerations for conservation
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ABSTRACT: Canada yew (Taxus canadensis Marsh.) is a gymnosperm that grows in the understory of mixed and deciduous forests of northeastern North America. This shrub had no economic importance until the discovery of paclitaxel, or TAXOL®, which is a compound found in plant tissue and used in cancer treatment. With the intensifying harvesting pressure on natural populations of this species, the natural gene pool might be affected. The objective of this study was to estimate the levels of genetic diversity and population structure in Canada yew, before any sizeable effects resulting from harvesting appear. Six natural populations of Canada yew were sampled in Quebec. Genetic diversity was estimated at 22 loci coding for 12 enzyme systems. At the population level, the number of alleles per locus was 1.32, the percentage of polymorphic loci was 26.5%, and the observed heterozygosity was 0.102. These results show that Canada yew is genetically less diverse than other yew species and the great majority of gymnosperms. However, the amount of population differentiation was substantially higher (FST = 10.2%) than that for other conifer and tree species growing in the boreal-temperate zone. Hypotheses related to the biogeography of the species and a likely metapopulation structure are proposed to explain the observed trends.Canadian Journal of Forest Research 02/2011; 31(1):110-116. · 1.68 Impact Factor -
Article: Low genetic diversity at allozyme loci in Juglans cinerea
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ABSTRACT: Butternut (Juglans cinerea L.) is a minor component of the temperate deciduous forest region of northeastern North America, but it is severely affected by the butternut canker (Sirococcus clavigignenti-juglandacearum Nair, Kostichka, and Kuntz) in the southern part of its natural range. Genetic diversity and population structure in as-yet unaffected or only slightly affected natural populations were evaluated at 12 isozyme loci. The genetic diversity estimates were low with values much below those estimated in other species of the same genus or in boreal tree species, with 25 and 13.9% polymorphic loci at the species and population levels, respectively; 1.3 and 2.3 alleles per locus and per polymorphic locus, respectively, at the species level; and an average observed heterozygosity of 0.028. Population differentiation was low, with the exception of one unique population. The implications for advanced conservation are discussed.Key words: butternut, isozymes, Sirococcus, canker, population structure.Canadian Journal of Botany 02/2011; 78(9):1238-1243. · 1.40 Impact Factor
