Genotyping Services for Molecular Breeding In Developing Countries: Opportunities and Perspectives.

The recent generation of markers such as SSRs and SNPs markers has been widely used in the studies of plant sciences such as genetic diversity, gene mapping, association studies, and tagging the genes of interest for marker-assisted selections in crop breeding programs. However, these molecular marker technologies are less accessible in developing countries than in developed countries because of factors including lack of skilled human resources , suitable infrastructure to support genotyping laboratories, and available funds. In order to alleviate these problems, the Genotyping Support Service (GSS) was created at the Generation Challenge Programme (GCP) in 2007 by collaborating with laboratory service providers worldwide that have the state-of-the-art technologies for molecular genotyping. This GSS program facilitates the access to these technologies by the agricultural research & development organizations in developing countries. The GSS not only bridges the cost-efficient genotyping services with our customers but also provides support and training for data analysis in order to properly interpret the genotypic and phenotypic data.

Since August 2007, GCP has launched a total of 3 calls for research grant applications of GSS projects. A total of 174 applications have been received and 73 of them have been awarded as molecular genotyping projects with SSR, SNP markers as well as DArT markers. The awarded research projects with topics from genetic diversity studies to marker-assisted selections have covered 14 crops from 25 countries.

As a very abundant genetic marker that can be automated for high-throughput genotyping, the SNP markers can greatly increase the speed, efficiency and cost-effectiveness of genotyping. Accordingly, GCP is gradually transitioning the marker services from SSR to SNP markers. The GCP has chosen KBioscience’s KASPar system as its main platform for SNP genotyping for breeding applications. So far, between 1,000 and 2,000 SNPs has been converted into this system for SNP genotyping of each of seven crops of critical importance to developing countries.

With the parallel development of the Integrated Breeding Platform (IBP), the GCP will provide the developing country breeding programs with easier access to more convenient genotyping services to support molecular breeding schemes such as MAS, MABC, MARS, and GWS.