Seed World

Communal SNP panels are the Ultimate Win for all Plant Breeders and Researchers

Source: Agriplex

AgriPlex Genomics continues to make genotyping services more accessible and affordable to all through their communal genotyping program, AgriPlex Connect (APC). The program made its debut last spring, offering a unique opportunity for the ag community to use PlexSeq SNP panels at a discounted price with a faster turnaround. 

The origins of these SNP panels come from ongoing collaborations between AgriPlex Genomics and the wider agricultural research community. AgriPlex Genomics coordinates the assembly of crop and livestock-specific consortia who work together to create a comprehensive SNP panel for the respective organisms. Each panel is aimed to provide a set of markers that can be used for various types of association studies including: breeding applications, genetic diversity studies, trait association, varietal ID and genetic purity analysis. 

After gathering community input and assessing collective genotyping needs, AgriPlex Genomics creates PlexSeq SNP panels, which are intended to be used by academia, public sector, industry research and breeders who share genotyping interests for a specific crop, or QA/QC in support of seed production and trade. 

The AgriPlex Connect program is quite simple: AgriPlex Genomics announces pre-set deadlines for specific panels to be run in their laboratory. Anyone who submits their samples on time receives exclusive AgriPlex Connect benefits, such as complimentary DNA extraction for all samples submitted and an expedited turnaround of 2-3 weeks. Additionally, AgriPlex Genomics offers a collective discount based on total community participation for that panel run. 

“It’s not so much the number of SNPs that drives the cost of genotyping panels. The real driver of cost is the number of samples being run. What we realised is that, if we could offer customers a way to combine their samples in a single sequencing run, we could reduce the cost per sample for everyone,” says Beni Kaufman, Director of Business Development at AgriPlex Genomics.

So far, community feedback for AgriPlex Connect has been overwhelmingly positive, as the group submissions have enabled them to save a significant amount of time and expenses.

“It’s a win-win for everyone. There isn’t any risk or cost to participate and is mutually beneficial for all involved. The price for genotyping projects can only decrease from what is initially quoted,” Kaufman says. 

Mark your calendars for panels being run through the AgriPlex Connect program this year: 

  • IRRI RiCA V4 (Rice) – Deadline March 31
  • 1K Soybean Community – Deadlines February 28, July 15, and August 31
  • Fresh Market Tomato – Deadlines April 30, May 31
  • LSU500 US Rice – Deadlines June 15, December 15
  • LSU80 QA/QC Rice – Deadlines July 31 and November 30
  • IRRI RiCA V5 (Rice) – Deadlines September 15, November 15
  • TBD – open to community input! 

A panel is only as useful as the SNPs that define it. As such, panels undergo continuous updating. Being part of the consortium allows participants an active hand in determining which traits should be included in the panel. Additionally, consortia members have the opportunity to provide input on the most beneficial dates for running the AgriPlex Connect program for their crop or livestock of interest.  If you are interested in submitting through the AgriPlex Connect program, joining a pre-existing consortium, or are interested in creating a consortium for a new crop, please fill out this brief interest form or email today!