White Spruce SNPs
An atlas of over 200,000 gene SNPs has been developed for white spruce (Picea glauca), with a true-positive rate of 92% (Pavy et al 2013a). These high-confidence SNPs are representative of over 17,000 expressed genes following the catalog of white spruce expressed genes (Rigault et al 2011; ftp://ftp.gydle.com/pub/arborea). True-positive rate has been determined with genotyping using high throughput Illumina Infinium chips (Pavy et al 2013b). Work is underway to expand this resource. High-confidence SNPs have been deposited in the public repository dbSNP of NCBI (https://www.ncbi.nlm.nih.gov/SNP/snp_viewBatch.cgi?sbid=1058878).
A discovery population of 1694 trees representative of 214 open-pollinated families from 43 natural populations was phenotyped for 12 wood and growth traits and genotyped for 6385 single-nucleotide polymorphisms (SNPs) representative of 2660 annotated gene sequences. Genotyping data are accessible through the Dryad Digital Repository https://doi.org/10.5061/dryad.6rd6f
Black Spruce SNPs
An atlas of nearly 100,000 gene SNPs has been developed for black spruce (Picea mariana), with a true-positive rate of 96% (Pavy et al 2016). These high-confidence SNPs are representative of nearly 15,000 genes following the white spruce nomenclature of expressed genes (Rigault et al 2011). True-positive rate has been determined with genotyping using a high throughput Illumina Infinium chip (Pavy et al 2016). SNPs have been deposited in the public repository dbSNP of NCBI (https://www.ncbi.nlm.nih.gov/SNP/snp_viewBatch.cgi?sbid=1059737).
Norway Spruce SNPs
A resource of more than 60,000 gene SNPs has been developed for Norway spruce (Picea abies), as well as a high throughput Illumina Infinium chip (Azaiez et al 2018). These high-quality SNPs are representative of nearly 14,000 genes following the white spruce nomenclature of expressed genes (Rigault et al 2011). The annotated SNP resource is available at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5247-z under Additional file 1.
A total of 726 trees were genotyped using an Infinium iSelect SNP array de 5571 SNPs representing as many distinct annotated genes, which was assembled from a catalog of high-confidence gene SNPs obtained from exome capture and sequencing (Azaiez et al., 2018). SNP data and the description of the genotyping array were deposited in the European Variation Archive (EVA, https://www.ebi.ac.uk/eva/, accession number PRJEB27427).
Work is underway to produce similar sets of gene SNPs for Sitka spruce (Picea sitchensis) and Engelmann spruce (Picea engelmannii).