b'PARTNER CONTENTLSU turns to mid-density multiplexing for quick and cost-effective molecular screening T he Louisiana State University (LSU) Ag-Centers ricesamples to Agriplex Genomics. Turn-around is longer than if we program is a small, applied breeding program generatingdid it in-house, but its quick enough for what we need. Since they big results. Currently about two thirds of the rice grownare very specialized, they can generate data cheaper than we can in Louisiana was bred by LSUs program. But LSU plant breederin-house.professor Adam Famoso knows theres no room to sit back andWhile Agriplex can screen genomes on an as-needed basis celebrate past successes: facing intense global competition, Loui- for any client, the most cost-effective way to work with a regular sianas farmers and millers are depending on the LSU team to rollclient is via a custom-made multiplexing panel. For the past two out higher yielding, more disease resistant, better quality variet- years, LSU and Agriplex have worked together to create and then ies. Thats why LSU has turned to new mid-density multiplexingstreamline a custom panel for LSUs rice program. The rice panel technology that allows better, faster, cheaper genomic screening.includes key single-gene traits but is also designed to help zero in LSU has the capacity to handle genomic screening in-houseon the complex traits most critical to farmers and millers, specifi-for simple traits that are associated with single genes, like diseasecally yield, milling characteristics, and certain morphological resistance, aroma, or leaf pubescence. However, LSUs rice pro- traits. To date, Famosos team has used the panel to evaluate well gram is now at the point where it requires more intensive multi- over 10,000 lines. He expects to scale up to between 10- and 15,000 plexing for more complex traits.lines per year. Initially we focused on low-hanging fruit where we could getWe are able to generate predictions on lines much, much immediate impact, says Famoso. But our goal when we startedmore cheaply than we could evaluate them in the field. The panel was to get to where we are now, which is looking for some of thehas made our lives much easier and our programs run faster, more complex traits like yield and quality that arent associ- Famoso says.ated with a single gene. The approach wealong with a lot of theThe LSU rice panel started with 1200 SNPs. The team then cut industry - has moved towards is genomic selection. Were notthat to what they thought were the most critical 550 SNPs. From trying to identify a gene per se; were trying to predict how well athere, the panel continues to be tweaked via further additions line will perform based on a larger number of genetic markers. Toand subtractions.enable this, we began collaborating with Kelly Robbins and SusanThe more the team utilises the panel, the more precise it will McCouch at Cornell University, who are experts in this field. Webecome, says Famoso. A panel doesnt have to be perfect right also hired a postdoctoral associate, Chris Hernandez, who isoff the batthats not the point. You want a starting place so that leading this research. the rest of your program can get going, and then you adjust from While singleplex screening cant provide broad enough data tothere. Maybe there are 60 SNPs that really dont do much, so lets screen for complex traits, high density multiplexing is too detailedget rid of those, but maybe we have key limitations elsewhere,and too expensivefor LSUs needs. To achieve the mid-densityso lets add some back in. The benefit of the Agriplex platform is sweet spot screening they need, LSU turned to Agriplex Genomics.theres flexibility.There have been good solutions for high density and lowOutsourcing molecular screening just makes sense, he adds. density for a number of years. Just recently, theres now cost- We need to stay focused on and invest our energies into what effective solutions for mid-density, says Famoso. For mid-sizewere doing with our research program. Everything else, Im genomic screening, say a few hundred markers, we send ourhappy to outsource. JUNE 2021SEEDWORLD.COM /37'