Optimizing a High-Throughput SNP Genotyping Workflow for Rice Improvement

The Genotyping Services Laboratory (GSL) has been established at IRRI to mainstream marker-assisted selection into rice breeding programs by providing rapid and cost-effective marker services. A high-throughput sample preparation workflow with an integrated LIMS for sample tracking is now being optimized.  The PlantTrak system for barcoded leaf sampling is being tested for rapid collection of tissue, followed by magnetic bead-based DNA extraction using a KingFisher system.  Genotyping of trait-specific markers targeted to specific QTLs and genes is currently performed using sets of 24 SNPs run on a Fluidigm EP1 system.  Diversity analysis, SNP fingerprinting and QTL studies at IRRI have primarily used genome-wide scans with 384-plex GoldenGate assays, while higher resolution scans now employ an Illumina Infinium 6K SNP chip for rice developed by Susan McCouch at Cornell University. User-friendly SNP data formatting and analysis tools have also been developed and are now available through the online IRRI Galaxy bioinformatics resource.  However, more work is needed to refine the SNP databases and informatics tools required for analysis of NGS and high-density marker data sets to facilitate a new era of precision breeding.