TraitGenetics has been established in 2000 and currently has a staff of 25 employees. The company is mainly involved in the development of molecular markers and marker analysis in crop plants. Molecular markers are diagnostic tools that are being used in plant breeding to identify and follow the inheritance of qualitative (monogenic) and quantitative (polygenic) traits during crossing and selection. With such markers plants can be selected at a very early stage of the growth cycle, saving time and costs for the plant breeder (smart breeding).

Our marker development activities in diploid plant species focus on the identification of single nucleotide polymorphism (SNP) markers. TraitGenetics specifically emphasizes the development of markers useful within current breeding material so that such markers can directly be applied by plant breeders. For polyploid species, where SNP marker development is still difficult and in its infancy, we perform microsatellite marker development and analyses with thousands of proprietary markers (oilseed rape and wheat). Over the recent years, we have gathered experience in many important field and vegetable crops. We have identified SNP markers in several thousand genes from maize sugar beet, the Brassica vegetables, sunflower, pepper and tomato. Our optimized SNP identification pipeline enables us to investigate routinely thousands of genes/ ESTs per month for the presence of SNPs through comparative sequencing at very reasonable costs. Recently, we have succeeded in using novel high throughput sequencing technologies (Illumina/ Solexa) to reliably identify SNPs and SNP haplotypes in thousands of genes simultaneously.

Furthermore, TraitGenetics has experience and high-throughput capacities to map large number of markers in crop plants. Over the last two years, we have mapped several thousands of genes and/ or SSR markers each in large segregating populations of several crop species. Our microsatellite analysis capacities (>1 million datapoints per year) permit the generation of large marker databases.

TraitGenetics has generated SSR marker databases in the polyploid oilseed rape and wheat with more than 250,000 datapoints each (>1,000 lines with 200-250 markers). In the area of SNP analysis, we have established a number of technologies that permit the analysis of large numbers of individual SNP markers (TaqMan and Pyrosequencing) as well as the analysis of SNP markers in a highly multiplexed fashion (SNPlex and Illumina Golden Gate) with capacities up to many millions of data points. At present, TraitGenetics focuses mainly on the development of standardized and optimized SNP multiplexes based on its large proprietary SNP databases for many different crop species.

Our further experience includes the rapid analysis of specific candidate genes for the association of markers/haplotypes with specific traits (association genetics) and other marker-related activities ranging from primer development to bioinformatic data analysis. With our experience, TraitGenetics mostly serves the international plant breeding community and has its customers among major plant breeding companies, academic institutions and other companies in the area of plant research to which we license our markers and Know-How, perform contract research and marker analysis services.

Large-Scale SNP and Haplotype Identification in Maize

In a recent project, TraitGenetics identified SNPs in 10,000 maize genes which corresponds to 25% of all maize genes.

Nearly 75,000 high quality SNPs were identified and the haplotype structure of each gene was analyzed.

With these data, TraitGenetics is currently developing highly multiplexed SNP assays that can be used for the simultaneous analysis of thousands of maize SNPs and genes in breeding material for such purposes as association genetics and germplasm characterization.