Seed World

Faster, More Efficient Quality Control in Maize is Just the Start

Maize is one of the most important multi-purpose crops worldwide, utilized for food, feed, fuel, and a variety of industrial products. In Africa and Latin America, maize is a staple food source for both humans and animals. In the US, demand for maize as a food option has increased 300% since the 1970s, mostly due to the popularity of both Hispanic and gluten-free food options. Maize, of course, is just one of many high-priority crops that requires efficient, cost-effective seed quality assurance (QA) and quality control (QC) to meet increasing market demand for high quality seed in the United States and globally. These requirements are more possible to meet now than ever thanks to AgriPlex Genomics mid-density genotyping PlexSeq technology.  

Corn seed quality is evaluated along many axes, but to maintain the desired distinct genetics over generations it is essential to assess the genetic purity of parental inbred lines and resulting hybrids during breeding operations and along the supply chain. Genetic purity testing has traditionally required time-consuming and expensive grow out tests. More recently, seed QA/QC has shifted to single nucleotide polymorphisms (SNP)-based testing. SNPs are heritable and distributed throughout eukaryotic genomes and are independent of the environment, reproducible, and present at all developmental stages. Further, they probe known positions in the genome, and may be linked to traits of interest. For these reasons SNPs are used as molecular markers for both molecular breeding applications and accurate, efficient, and cost-effective QA and QC testing.

While high-density SNP chip arrays that can interrogate many SNPs per DNA sample have been developed and commercialized in multiple crops, these high-density SNP tools were developed mostly to satisfy molecular breeding requirements. For effective quality testing, informative, high-throughput, and cost-effective mid-density genotyping is a better fit. 

Enter PlexSeq: a multiplexing technology for mid-density SNP genotyping based on amplicon sequencing, which decreases both the time and cost of genotyping. PlexSeq offers an artificial intelligence multiplexing algorithm, which can design all possible primers around any SNP of interest and identify optimal sets of primers that can be mixed in just one PCR amplification reaction. Once the amplifications are complete, the amplicon libraries are mixed and subjected to one bead clean-up and loaded onto the sequencer. The PlexSeq process requires minute quantities of crude DNA isolatable from a variety of tissues. The process is amenable to automation; all steps can be conducted on liquid handlers and high-capacity thermocyclers, enabling high throughput genotyping. AgriPlex Genomics’ vast collection of barcode combinations permits simultaneous sequencing limited only by the sequencer’s capacity. 

To optimize efficiency further, AgriPlex Genomics in collaboration with various partners have created multiple crop specific ‘panels’ – sets of validated markers developed for specific applications. For maize QA/QC, Agriplex Genomics built onto a maize panel created by the International Maize and Wheat Improvement Center (CIMMYT). The 131 SNP panel allows the generation of a unique SNP profile for every corn line, making it possible to tell any two lines apart and detect off-types within a line. The panels are dynamically alterable and customizable as the germplasm evolves and priorities shift. 

Assessing genetic purity using PlexSeq methodology in conjunction with the maize quality SNP panel provides a generic tool fit for quality testing across the genetic width of maize. The operational efficiency and cost-effectiveness of PlexSeq provides a generic global solution to all QC/QA needs. The Maize QC SNP panel is available as a service from AgriPlex Genomics and is also available as a kit to be used by in-house genotyping laboratories.

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