Seed World

Multiplexing: The Less Expensive, More Efficient QA Solution

When it comes to quality assurance (QA), there are two options available to seed breeders and companies. The tried-and-true, traditional option is to run every genetic purity, trait confirmation, adventitious presence, and varietal ID test separately. If, for example, you wanted to confirm correct zygosity in 60 lines using this system, you’d sample 200 individuals from each line, testing for zygosity of every trait of interest, for a total of 1200 reactions per trait. If you wanted to test for varietal ID, adventitious presence, and genetic purity, you’d run each test individually. While this kind of QA technology is one of the key reasons plant breeding – and agriculture as a whole – has made such huge leaps and bounds forward in the last few decades, it can be costly, cumbersome, and expensive in supplies and manhours. 

There is another option. Mid-density multiplexing technology makes it possible to test for multiple traits simultaneously within a single reaction. In fact, multiplexing allows the targeting of multiple QA outcomes into a single test panel. Not surprisingly, streamlining multiple traits and/or multiple outcomes into a single reaction means multiplexed QA is far faster, more efficient, more comprehensive and – yes – less expensive than the traditional one-at-a-time option. 

Multiplexing’s efficiency opens opportunities for additional checkpoints throughout the breeding and/or production process. For example, during variety development, multiplexing allows simultaneously testing in the same reaction for adventitious presence and trait confirmation, that is, testing for unwanted genetics early and often to reduce contamination set-backs, while at the same time testing for the presence of the desired traits of interest and driving their introgression into elite genetic backgrounds in a significantly more efficient and informed fashion. 

More and more companies are committing to testing for genetic purity early in the life cycle of a product, starting in the research phase through breeding and in all production lots. Companies are turning to multiplexing to have efficient purity assurance as it provides opportunities for additional streamlining. For example, multiplexing could open opportunities to bring a company’s research and supply/production sides – traditionally entirely separate – much closer together. 

Multipurpose multiplexed SNP panels that consist of markers for genomic screening, trait associated markers and varietal ID markers, such as the Rice Custom Amplicon SNP panel (RiCA V4 by IRRI and Agriplex Genomics) are an example for a multiplex that serves both the breeder and the seed producer. These panels can evolve still by creating nested panels, that is, using markers that serve both applications (for example, when a given SNP marker is useful for both breeding application and identification – thus reducing the number of markers needed to genotype and consequently the price.) 

Yes, multiplexed QA is a very different way of thinking. But, as more and more labs and seed production plants get excited about the potential and opportunity it offers, there’s little question that multiplexed QA is the direction our industry is heading.