Applying Sequencing and High-Throughput SNP Genotyping to Accelerate Progress in Rice Breeding

We are currently developing a high-throughput SNP genotyping service at IRRI to support the needs of rice research and breeding programs within the Global Rice Science Partnership by providing rapid and cost-effective marker services. Deep sequencing of key donors and breeding lines is now being performed to assist with SNP marker development.  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.  Over the past 5 years, 384-plex GoldenGate assays on an Illumina BeadXpress Reader have been used for diversity analysis, SNP fingerprinting and QTL studies at IRRI.  More recently, an Illumina Infinium 6K SNP chip for rice developed by Susan McCouch at Cornell University was deployed at IRRI to obtain high-density marker data for characterizing breeding populations and genetic stocks.  At the same time, genotyping by sequencing (GBS) approaches, including barcoding 96 and 384 samples per sequence lane, are being evaluated in comparison to SNP array technology based on number of loci, call rates, turnaround times, and cost per sample. Future efforts will focus on large-scale application of GBS on breeding materials to enable QC variety identification, tracking of donor introgressions, and integration of genomic selection into the mainstream breeding programs.