SNP Genotyping to Accelerate Rice Breeding

We are developing a high-throughput SNP Genotyping Services Lab at IRRI to support the needs of rice breeding programs within the Global Rice Science Partnership.  Efficient target selection using trait-specific SNP markers is provided using a 192.24 Dynamic Array IFC with the Fluidigm EP1 system.  For genome-wide scans, we have explored a number of different systems to evaluate the SNP number, call rates, turn-around times, ease of analysis, and cost per sample for each platform.  At the low end, sets of 96 genome-wide SNPs on Fluidigm are being tested for low-cost quality control of seed lots.  Over the past 5 years, a large number of samples have also been run with 384-SNP sets on the Illumina BeadXpress Reader, which provided reasonable power and resolution for diversity analysis, QTL mapping, and background selection.  More recently, an Illumina Infinium rice 6K SNP chip developed at Cornell University has been deployed at IRRI to provide high resolution genome-wide scans for SNP fingerprinting, QTL analysis, and introgression mapping.  At the same time, we have compared results with outsourced genotyping by sequencing (GBS) to evaluate if the higher resolution and low cost of GBS outweighs the disadvantages of long turnaround times and high levels of missing data.  Current activities include testing GBS in-house and sequencing of parental lines in the breeding programs.  Future efforts will also focus on testing improved analysis pipelines and developing user-friendly informatics tools for analysis of large marker data sets to facilitate a new era of precision breeding.