Sequence-based Genotyping for Marker Discovery and Co-dominant Scoring in Germplasm and Populations

Fixed-content SNP genotyping platforms are available for a number of species, which often represent only a fraction of genetic diversity present in the germplasm. In this context, and to enable cost-efficient genotyping in a broad range of species, we have developed Sequence-Based Genotyping (SBG) for simultaneous marker discovery and co-dominant scoring using next-generation sequencing (Truong et al. 2012). The most distinguishing features of SBG are the ability to genotype samples independent of population structure and regardless of whether parental data is included. Furthermore, SBG allows to co-dominantly score SNP markers segregating in populations, without the need for a reference sequence.  A simple sample preparation workflow with an adjustable genome complexity reduction is available and is offered as an easy to use kit. As an example to demonstrate and to further develop the capabilities of SBG, we performed marker discovery and genotyping in tomato and a number of additional vegetable and field crop species. Multiple subsets of the genome were generated and mined for SNPs. Filtering of the SNP datasets produced over 1,000 high quality SNP markers for each subset of the genome. Mapping of the SNP containing loci to the tomato genome sequence showed that the SNP markers were randomly distributed across the genome and that each genome subset targets a different set of SNP loci.

We show that SBG provides users with the utmost flexibility in gathering multiple sets of high quality markers that can be directly used for genotyping and various downstream applications, such as genetic mapping, genetic diversity analysis, trait mapping and direct mapping to reference genome sequences

The SBG technology is covered by patents and patent applications owned by Keygene N.V.