title: Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs.
abstract: BACKGROUND
  High-throughput genotyping technologies represent a highly efficient way to accelerate genetic mapping and enable association studies. As a first step toward this goal, we aimed to develop a resource of candidate Single Nucleotide Polymorphisms (SNP) in white spruce (Picea glauca [Moench] Voss), a softwood tree of major economic importance.
  
  
  RESULTS
  A white spruce SNP resource encompassing 12,264 SNPs was constructed from a set of 6,459 contigs derived from Expressed Sequence Tags (EST) and by using the bayesian-based statistical software PolyBayes. Several parameters influencing the SNP prediction were analysed including the a priori expected polymorphism, the probability score (PSNP), and the contig depth and length. SNP detection in 3' and 5' reads from the same clones revealed a level of inconsistency between overlapping sequences as low as 1%. A subset of 245 predicted SNPs were verified through the independent resequencing of genomic DNA of a genotype also used to prepare cDNA libraries. The validation rate reached a maximum of 85% for SNPs predicted with either PSNP > or = 0.95 or > or = 0.99. A total of 9,310 SNPs were detected by using PSNP > or = 0.95 as a criterion. The SNPs were distributed among 3,590 contigs encompassing an array of broad functional categories, with an overall frequency of 1 SNP per 700 nucleotide sites. Experimental and statistical approaches were used to evaluate the proportion of paralogous SNPs, with estimates in the range of 8 to 12%. The 3,789 coding SNPs identified through coding region annotation and ORF prediction, were distributed into 39% nonsynonymous and 61% synonymous substitutions. Overall, there were 0.9 SNP per 1,000 nonsynonymous sites and 5.2 SNPs per 1,000 synonymous sites, for a genome-wide nonsynonymous to synonymous substitution rate ratio (Ka/Ks) of 0.17.
  
  
  CONCLUSIONS
  We integrated the SNP data in the ForestTreeDB database along with functional annotations to provide a tool facilitating the choice of candidate genes for mapping purposes or association studies.
authors.affiliation: Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada. nathalie.pavy@rsvs.ulaval.ca
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pavy
authors.forename: Lee S
authors.initials: LS
authors.lastname: Parsons
authors.forename: Charles
authors.initials: C
authors.lastname: Paule
authors.forename: John
authors.initials: J
authors.lastname: MacKay
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001499:Bayes Theorem; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D008969:Molecular Sequence Data; D028222:Picea / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D018076:DNA, Complementary