Developing a High-Throughput SNP Genotyping Workflow to Support Breeding Applications in Rice

Recent advances in single nucleotide polymorphism (SNP) marker technologies have the potential to enable rapid and cost-effective genotyping of large numbers of DNA samples for breeding applications.  We are currently developing a high-throughput SNP genotyping workflow at the Molecular Marker Applications Lab at IRRI to support the marker genotyping needs of rice breeding programs under the Global Rice Science Partnership.  An improved sample preparation workflow is being optimized to increase the efficiency of rice leaf tissue sampling, DNA extraction, and DNA quality control and normalization in preparation for SNP genotyping.  Validated markers from the 44K SNP chip developed at Cornell University are being used to select subsets of informative SNPs for different germplasm groups and genome regions.  A 384-plex SNP set for Indica germplasm and a 384-plex SNP set for Indica/Japonica material were developed as GoldenGate VeraCode assays for the Illumina BeadXpress Reader and were further optimized by replacing poor performing SNPs after testing on diverse rice accessions at IRRI.  Pilot studies were successfully performed using the 384-SNP sets for genetic diversity analysis, QTL mapping, and marker-assisted selection, and SNP fingerprint databases are currently being developed to enable rapid variety identification.  For applications requiring fewer SNP markers, we are also testing the Fluidigm EP1 System using Dynamic Array chips with sets of 24, 48 and 96 SNPs to enable rapid, low-cost assays for running SNP markers targeted to specific chromosomal regions and genes controlling traits of interest.