title: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana).
abstract: Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes 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.
authors.affiliation: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.|Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pavy
authors.affiliation: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.|Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: France
authors.initials: F
authors.lastname: Gagnon
authors.affiliation: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.|Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Astrid
authors.initials: A
authors.lastname: Deschênes
authors.affiliation: Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Brian
authors.initials: B
authors.lastname: Boyle
authors.affiliation: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.|Natural Resources Canada, Canadian Wood Fibre Centre, 1055 Rue du P.E.P.S., PO Box 10380, Station Sainte-Foy, Québec, QC, G1V 4C7, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Beaulieu
authors.affiliation: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.|Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
mesh_terms: D002170:Canada; D059472:Exome; D014644:Genetic Variation; D060005:Genotyping Techniques / Q000379:methods*; D028222:Picea / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: Infinium SNP genotyping array; conifers; exome capture; genomic probes species transferability; in silico SNPs; population genomics