SNP Genotyping to Accelerate Rice Breeding

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 has been optimized to increase the efficiency of leaf tissue sampling and DNA extraction in preparation for genotyping.  Multiple sets of 24 and 96 SNPs on a Fluidigm EP1 system are being used for rapid genotyping of markers targeted to specific QTLs and genes controlling traits of interest, including gene-based SNPs, top GWAS hits, and flanking markers selected from 44K SNP data.  Legacy SSRs and functional indel markers are being genotyped on a 96-capillary Fragment Analyzer.  Diversity analysis, SNP fingerprinting and QTL studies primarily use genome-wide scans with fixed sets of 384-SNPs, while high-resolution scans using a 6K SNP chip developed at Cornell University are being employed to obtain high-density marker data for breeding populations and specialized genetic stocks.  At the same time, genotyping by sequencing (GBS) approaches are being compared to the 6K SNP data to evaluate the relative advantages of each platform for SNP number, call rates, turn-around times, ease of analysis, and cost per sample.  User-friendly SNP data formatting and analysis tools have also been developed and are now available through the online IRRI GSL-Galaxy bioinformatics resource.  The GSL is focused on providing high quality services with fast turn-around times for rice research and breeding programs at IRRI and partners across the world.