Rice (Oryza Sativa) is the single most important food crop to human nutrition and caloric intake, providing more than 20% of all calories consumed by humans worldwide. Because managing and improving the quality of rice is so crucial to our ability to feed the growing human population, efficient, cost-effective seed quality assurance (QA) and quality control (QC) is vital. Meeting these requirements is increasingly possible thanks to AgriPlex Genomics’ mid-density genotyping PlexSeq technology.
Single nucleotide polymorphisms (SNP)s, which are heritable, codominant, and distributed with relatively high frequency throughout plant genomes, have proven the fastest and most cost-effective molecular marker to assess genetic purity, varietal identification, trait confirmation, and adventitious presence parameters without the need for grow-outs.
In 20xx, Dr. Adam Famoso, associate professor at Louisiana State University’s Rice Research Station, developed a panel of 80 validated SNP markers called LSU80 for improved and expedited QA and QC.
The LSU80 panel can be divided into two marker groups:
The first group consists of 48 genome-wide markers and include markers that were previously used for U.S. rice purity fingerprinting. The SNPs in this group are spread throughout the rice genome and were put together to distinguish any two US rice varieties from each other. The number of markers per chromosome varies from 1 – 7 SNPs, with the average distance of 6.8 Mb between two adjacent SNPs.
The second group of 32 SNPs includes all presently known trait associated markers relevant to the U.S. rice. Of these, 12 SNPs are associated with various disease resistances, such as rice blast (Pita, and Pi genes) and leaf blight (CRSP2.1). Other markers are tied to fertility restoration- a trait crucial to hybrid rice production, plant and seed morphology, flavor, and cooking quality.
For added efficiency, the panel can be used in combination with PlexSeq technology: 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.
The LSU80 panel implemented at AgriPlex Genomics provides an efficient, cost-effective solution for seed QA/QC applications during breeding operations and along the supply chain. The ability to simultaneously probe an optimal number of markers across large number of samples provides a reliable snapshot of the germplasm’s genetics while enabling one to address varietal identity and genetic purity of the line and confirming the presence of many traits of interest. The flexibility of the platform enables continual revision and updating of the marker set, ensuring it keeps pace with current trait development, needs, and evolving regulatory requirements landscape.
The LSU80 rice 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.
