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

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.

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

“…In total, 80% of the 2652 genotyped genes had a predicted function or protein domain and at least one assigned GO term, and the remaining 20% were of unknown function or had no GO term, as reported in Pavy et al . (2013). In the set of 1120 genes associated with the different wood properties, 88% had an assigned GO term and 80% had an assigned Pfam.…”

“…Discovery of the SNPs, genotyping methods and quality control criteria were described previously (Pavy et al ., 2013; Beaulieu et al ., 2014). Briefly, for each of the 1694 trees, DNA was extracted from foliage and individuals were then genotyped with the Illumina Infinium HD iSelect bead chip PgAS1 at a rate of 50 ng μl −1 previously described by Pavy et al .…”

“…Briefly, for each of the 1694 trees, DNA was extracted from foliage and individuals were then genotyped with the Illumina Infinium HD iSelect bead chip PgAS1 at a rate of 50 ng μl −1 previously described by Pavy et al . (2013). The SNPs were from candidate genes belonging to 1868 gene families as described by Pavy et al .…”

“…Our aim was to delineate the genetic architecture of wood traits in white spruce ( Picea glauca (Moench) Voss) by testing a large panel of genes with diverse functions and expression profiles (see Pavy et al ., 2013) and integrate these findings with genome‐wide expression data to shed light onto the underlying gene networks (Fig. 1).…”

Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

“…Family-wise, there was 47% overlap between the two validation populations. DNA extraction for all the samples collected was conducted as reported in Pavy et al (2013).…”