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SNP Development
At TraitGenetics, SNPs are detected through comparative Sanger sequencing in a testpanel of individuals on an ABI 3730xl capillary sequencer. Sequences are assembled and automatically scanned for polymorphisms in our SNP pipeline software suite.
Each sequence alignment, along with all identified polymorphisms, is inspected visually by skilled personnel, resulting in a false calling rate of <5%. Allele frequencies of SNPs within relevant populations are determined through sequencing of DNA pools prepared from carefully quantified individual samples. This method provides data on flanking sequences required for subsequent assay design as well as haplotype information due to long sequence reads. 
 Example of polymorphism in inbred lines and pools 
TraitGenetics has available a large number of SNPs for analysis of most major crop plants. Unlike other polymorphism data currently available, these SNPs are all visually inspected, confirmed and validated by experienced personnel. All sequence and polymorphism data are accessible through mySQL databases. Following SNP identification, custom assay design and genotyping using TaqMan, Pyrosequencing, SNPlex or Illumina arrays is available upon request.
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