The 13,461 Picea glauca single nucleotide polymorphisms (SNPs) described in two articles by Pavy and collaborators in 2013 (BMC Biology 10:184 (27p.) and Molecular Ecology Resources (13 (2): 324-336) ) are now available in the Single Nucleotide Polymorphism Database of NCBI. SNP detection methods and genotyping results are described in the publications.
An atlas of 212,765 high-confidence SNPs
SNPs were detected among the sequences of several thousands of expressed gene sequences using Varscan software. Next-generation sequences were aligned on white spruce gene catalogue (GCAT) using Mosaik software. SNPs with minor allele frequency MAF < 0.01 were automatically discarded. The detection accuracy was verified with large genotyping datasets and indicated an overall high-confidence of the SNPs reported. These SNPs can also be accessed and retrieved from the Single Nucleotide Polymorphism Database of NCBI.
Enhancing genetic mapping of complex genomes through the design of high-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce
Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners
The landscape of nucleotide polymorphism amoung 13,500 genes of the conifer Picea glauca, relationships with functions, and comparison with Medicago truncatula