We published HD-Marker: a highly multiplexed and flexible approach for targeted genotyping

On December 04, 2018, Professor Zhenmin Bao's team at Ocean University of China have developed a high-throughput, sequencing-based GoldenGate approach called HD-Marker, allows highly multiplexed, targeted genotyping of more than 10,000 genes in a single-tube assay. The new technology, published in the journal Genome Research, addresses the array-related issues of original GoldenGate methodology and provides a tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.

The profiling of phenotype-related genetic variations lies at the heart of modern genetics. With abundant 'functional' marker resources having been accumulated, a diverse range of genetic research and applications are best achieved through target genotyping. However, targeted genotyping of these markers on a large scale (e.g., thousands to tens of thousands of markers) and in a cost-effective manner remains a major challenge especially for laboratories working on nonmodel organisms. Most of these approaches remain very costly for large-scale genotyping applications due to either a requirement for expensive, specialized instruments (e.g., RainStorm or Ion Proton systems) or high library preparation cost prior to capture. Illumina’s GoldenGate has been proposed as a promising tool for genotyping a large set of genomic loci and it is well known for its high SNP multiplexity and high flexibility of SNP selection. However, original GoldenGate builds on the BeadArray platform and suffers from several array-based limitations. 

Here, we develop a high-throughput, NGS-based GoldenGate approach (called HD-Marker) which switches GoldenGate from BeadArray to NGS platforms. This advanced method allows highly multiplexed, targeted genotyping of user-defined markers and is flexible in terms of both multiplex levels and marker types. With its remarkable cost-effectiveness (as low as $0.002 per genotype) and high flexibility in choice of multiplex levels and marker types, HD-Marker provides a highly attractive tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.

Professor Shi Wang from Ministry of Education Key Laboratory of Marine Genetics and Breeding was the corresponding author of this study. This research was granted by the National Key Research and Development Program of China, the National Natural Science Foundation of China, the major basic research projects of Shandong Natural Science Foundation, the Blue Life Breakthrough Program of LMBB, AoShan Talents Program of Qingdao National Laboratory for Marine Science and Technology, and the Fundamental Research Funds for the Central Universities.