Keygene SBG
Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations
Conventional marker-based genotyping platforms are widely available, but not without  their limitations. In this context, we developed Sequence-Based Genotyping (SBG), a  technology for simultaneous marker discovery and co-dominant scoring, using nextgeneration  sequencing. SBG offers users several advantages including a generic  sample preparation method, a highly robust genome complexity reduction strategy to  facilitate de novo marker discovery across entire genomes, and a uniform  bioinformatics workflow strategy to achieve genotyping goals tailored to individual  species, regardless of the availability of a reference sequence. The most distinguishing  features of this technology are the ability to genotype any population structure,  regardless whether parental data is included, and the ability to co-dominantly score  SNP markers segregating in populations. To demonstrate the capabilities of SBG, we  performed marker discovery and genotyping in Arabidopsis thaliana and lettuce, two  plant species of diverse genetic complexity and backgrounds. Initially we obtained  1,409 SNPs for arabidopsis, and 5,583 SNPs for lettuce. Further filtering of the SNP  dataset produced over 1,000 high quality SNP markers for each species. We obtained  a genotyping rate of 201.2 genotypes/SNP and 58.3 genotypes/SNP for arabidopsis  (n=222 samples) and lettuce (n=87 samples), respectively. Linkage mapping using  these SNPs resulted in stable map configurations. We have therefore shown that the  SBG approach presented provides users with the utmost flexibility in garnering high  quality markers that can be directly used for genotyping and downstream applications.  Until advances and costs will allow for routine whole-genome sequencing of  populations, we expect that sequence-based genotyping technologies such as SBG  will be essential for genotyping of model and non-model genomes alike.