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Next-generation sequencing
Currently high expectations are being placed on the next-generation sequencing technologies in providing cost efficient and highly effective systems towards the fast identification of large numbers of SNPs within a short time frame with little costs. 

TraitGenetics is currently evaluating most of the currently available systems (454, Illumina and SOLiD) for their data quality and accuracy in SNP identification and haplotype determination. In order to do this, we specifically compare data from thousands of genes that we have generated via comparative Sanger sequencing with data generated using next-generation sequencing technologies. We think that only by using sophisticated bioinformatics in combination with validated training sets, it will be possible to fully assess the potential of these technologies.

With the current lack of full genome sequences for most of the important crop and vegetable plants, it is at present not fully clear how high the accuracy of SNPs identified with the next-generation sequencing is and whether genome enrichment technologies can be used to accurately predict SNPs. A very low rate of falsely discovered SNPs is however essential concerning the final costs of developing, for example, large multiplex SNP assays with technologies and haplotype identification.

SNP identification
SNP identification in pools of lines of a specific amplicon using the Illumina technology
SNP identification

Allele frequency determination in pooled samples derived from amplicon resequencing with the Illumina next generation sequencing technology



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