b'PARTNER CONTENTFaster, More Efficient Quality Control in Maize is Just the StartBy: Benjamin (Beni) Kaufman, PhDM aize 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 increas-ing 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 main-tain 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 test-ing. SNPs are heritable and distributed throughout eukaryotic genomes and are independent of the environment, reproduc-ible, 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,ing. AgriPlex Genomics vast collection of barcode combinations and cost-effective QA and QC testing. permits simultaneous sequencing of large number of samples While high-density SNP chip arrays that can interrogate manylimited only by the sequencers capacity. SNPs per DNA sample have been developed and commercializedTo optimize efficiency further, AgriPlex Genomics in collabo-in multiple crops, these high-density SNP tools were developedration with various partners have created multiple crop specific mostly to satisfy molecular breeding requirements. For effectivepanels - sets of validated markers developed for specific applica-quality testing, informative, high-throughput, and cost-effectivetions. For maize QA/QC, Agriplex Genomics built onto a maize mid-density genotyping is a better fit.panel created by the International Maize and Wheat Improve-Enter PlexSeq: a multiplexing technology for mid-density SNPment Center (CIMMYT). The 131 SNP panel allows the generation genotyping based on amplicon sequencing, which decreasesof a unique SNP profile for every corn line, making it possible to both the time and cost of genotyping. PlexSeq offers an artificialtell any two lines apart and detect off-types within a line. The intelligence multiplexing algorithm, which can design all possiblepanels are dynamically alterable and customizable as the germ-primers around any SNP of interest and identify optimal sets ofplasm evolves and priorities shift. primers that can be mixed in just one PCR amplification reaction.Assessing genetic purity using PlexSeq methodology in con-Once the amplifications are complete, the amplicon libraries arejunction with the maize quality SNP panel provides a generic mixed and subjected to one bead clean-up and loaded onto the se- tool fit for quality testing across the genetic width of maize. The quencer. The PlexSeq process requires minute quantities of crudeoperational efficiency and cost-effectiveness of PlexSeq provides DNA isolatable from a variety of tissues. The process is amenablea generic global solution to all QC/QA needs. The Maize QC SNP to automation; all steps can be conducted on liquid handlers andpanel is available as a service from AgriPlex Genomics and is also high-capacity thermocyclers, enabling high throughput genotyp- available as a kit to be used by in-house genotyping laboratories.SEPTEMBER 2022SEEDWORLD.COM /43'