Seed World

New Partnership Offers Field-To-Result Mid-Density Genotyping Solutions

At Agriplex Genomics, our ambition is to provide the most innovative and reliable mid-density genotyping service available anywhere. That’s why we’ve recently formed a partnership with genomics data solutions company, NRGene. Individually, both of our companies boast molecular breeding decision making components: NRGene offers an optimized genotyping software solution and turn-key informatics; Agriplex delivers focused amplicon-based sequencing technology. Together, our partnership offers a fi eld-to-lab genotyping solution for labs that may need to initiate or enhance their molecular breeding programs.

NRGene covers a project’s front end. It begins with NRGene’s analytical solution – SNPer™. Even though it involves advanced algorithmics, the logic behind this solution is clear and simple: to minimize the number of data points measured per sample while maintaining the maximal amount of information provided. NRGene sequences and analyzes the full genomic diversity used in a breeding program to discover millions of SNPs segregating in the genetic pool. Next, they select a target set of SNPs representing genetic differences. They further reduce the target set of SNPs to the minimum need to genotype a massive number of samples. This minimal set is designed to allow for a “fill in the blanks” computational process called imputation. This process delivers the full target set for all samples. Since fewer data points are actually measured and the majority are computationally deduced, costs are greatly reduced.

Agriplex Genomics manages the project’s mid-field. The goal of imputation is to reduce a large, expensive assay to a more manageable and cost-effective size, 1,000 to 3,000 SNPs. For this range, Agriplex’s technology is the most optimized in the industry. We take the key SNPs from NRGene and develop a proprietary multiplexed assay using our PlexSeq technology. Then, we run this assay through our in-house robotics and next-generation sequencers. Our PlexCall analysis software then automatically produces a concise report of allele frequencies and SNP calls.

Lastly, NRGene handles the project’s final strides, translating our call results into predictive genomics and breeding program guidance. The received data goes back into NRGene’s platform which applies its imputation procedure and delivers the full SNP set for all samples. The SNP panels that are used can be flexibly adjusted to fi t more precisely to the specific populations and the evolution of the breeding program, for the benefit of next generations genotyping. And the cycle goes on…

“NRGene’s bioinformatic capabilities give us the DNA sequence information we require to develop a winning multiplexed assay,” says Scott Weigel, co-founder of AgriPlex Genomics. “But the real winners are the researchers, and breeders who benefit from complete datasets at a lower cost.”