Optimizing a High-Throughput Workflow for a Rice Genotyping Services Lab

The Genotyping Services Laboratory (GSL) was established at IRRI to mainstream marker-assisted selection into rice breeding programs by providing rapid and cost-effective marker services.  Current activities are focused on optimizing the high-throughput sample preparation workflow, including implementing a PlantTrak genetic sampling and barcoding system, configuring an integrated LIMS for sample tracking, and testing kits for automated DNA extraction in preparation for SNP genotyping.  Multiple sets of 24 SNPs on a Fluidigm EP1 system are being used for rapid genotyping of markers targeted to specific QTLs and genes controlling traits of interest. Genome-wide scans using 96 Fluidigm SNPs, 384 Goldengate SNPs, an Infinium 6K chip, and genotyping by sequencing (GBS) are being used for various applications, including diversity analysis, SNP fingerprinting, QTL studies, and background selection. A rapid system for extracting high quality DNA is a prerequisite to ensure reliable and efficient SNP genotyping. Three commercially available silica membrane kits using centrifugation and two magnetic bead-based kits using the Thermo KingFisher Flex were compared. DNA samples from the different protocols were checked for quality and quantity as part of the sample preparation workflow for Fluidigm and Infinium SNP genotyping. Finally, user-friendly SNP data formatting and analysis tools were also developed and are available through the online IRRI Galaxy bioinformatics resource.  The GSL is focused on providing high quality genotyping services with fast turn-around times for rice research and breeding programs at IRRI and its global partners. The latest information on our services can be found on our website (gsl.irri.org).