High-throughput SNP genotyping in rice using the Fluidigm EP1 system

The Genotyping Services Laboratory has been established at IRRI to provide rapid and cost-effective marker services for the rice research and breeding community.  We have deployed the Fluidigm EP1 system using SNPtype markers for running flexible sets of SNPs for rapid diversity analysis and for target and background selection during marker-assisted backcrossing.  SNP markers are currently being validated to target specific QTLs and genes controlling traits of interest, including gene-based SNPs, top GWAS hits, and flanking markers selected from 44K SNP data.  Sets of 24 gene-based and closely flanking SNPs for target loci are being run on 192.24 IFCs for essential genes for the breeding programs, including bacterial blight resistance, submergence tolerance, and grain quality traits.  In addition, 288 genome-wide SNPs known to be informative across indica germplasm were converted to SNPtype markers and are being used for polymorphism surveys on 96.96 Dynamic Array IFCs. We are focused on providing fast turn-around times for rice research and breeding programs at IRRI and partners in Southeast Asia and Africa.