SNP Data

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.

 

Publications

Polymorphe_SNPs genotyped_Goldengate

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

Polymorphe_SNPs_genotyped_ Infinium

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

SNPs_atlas_Pavy2013

The landscape of nucleotide polymorphism amoung 13,500 genes of the conifer Picea glauca, relationships with functions, and comparison with Medicago truncatula