DOI: 10.5061/dryad.tr87v
title: Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

description: Picea mariana is a widely distributed boreal conifer across Canada and the
 subject of advanced breeding programs for which population genomics and
 genomic selection approaches are being developed. Targeted sequencing was
 achieved after capturing P. mariana exome with probes designed from the
 sequenced transcriptome of Picea glauca, a distant relative. A high
 capture efficiency of 75.9% was reached although spruce has a complex and
 large genome including gene sequences interspersed by some long introns.
 The results confirmed the relevance of using probes from congeneric
 species to perform successfully interspecific exome capture in the genus
 Picea. A bioinformatics pipeline was developed including stringent
 criteria that helped detect a set of 97 075 highly reliable in silico
 SNPs. These SNPs were distributed across 14 909 genes. Part of an Infinium
 iSelect array was used to estimate the rate of true positives by
 validating 4267 of the predicted in silico SNPs by genotyping trees from
 P. mariana populations. The true positive rate was 96.2%, for in silico
 SNPs compared to a genotyping success rate of 96.7% for a set 1115 P.
 mariana control SNPs recycled from previous genotyping arrays. These
 results indicate the high success rate of the genotyping array and the
 relevance of the selection criteria used to delineate the new P. mariana
 in silico SNP resource. Furthermore, in silico SNPs were generally of
 medium to high frequency in natural populations, thus providing high
 informative value for future population genomics applications.
description: 29196_Reference_Picea_mariana_contigsReference Picea mariana contigs used for read mapping: contig number, length and nucleotide sequences.SNP_dataset_Varscan_software_part_01SNP dataset from Varscan software, part 1: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.SNP_dataset_Varscan_software_part_02SNP dataset from Varscan software, part 2: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.SNP_dataset_Varscan_software_part_03SNP dataset from Varscan software, part 3: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.SNP_dataset_Varscan_software_part_04SNP dataset from Varscan software, part 4: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.SNP_dataset_GS_reference_mapper_softwareSNP dataset from GS reference mapper software: contig number, SNP position, reference and variant alleles, total depth and variant frequency (VarFreq).Genotype_PmGP1_Natural_PopulationPmGP1 array genotyping results for all SNP accessions for trees from natural populations: genotypes for all SNPs of PmGP1 for trees from Picea mariana natural populations.