High-Throughput SNP Genotyping for Breeding Applications in Rice

We are currently developing a high-throughput SNP genotyping service at IRRI to support the needs of rice breeding programs within 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 in preparation for SNP genotyping.  Sets of informative SNPs for different germplasm groups and genome regions are being selected from the 44K SNP chip developed at Cornell University.  Fixed sets of 384 SNPs for Indica germplasm and 384 SNPs for Indica/Japonica material are now routinely used for genetic diversity analysis, QTL mapping, and marker-assisted backcrossing.  Likewise, SNP fingerprinting databases are being developed to support variety identification and diversity analysis.  Flexible sets of 24 and 96 SNPs on a Fluidigm EP1 system are being tested to enable rapid, low-cost genotyping of markers targeted to specific QTLs and genes controlling traits of interest, and to provide quality control tests to detect seed labeling errors.  Functional SNPs and allele-specific SNP haplotypes for breeding-relevant genes are being validated to provide custom sets of markers tailored to different rice breeding programs.  Genotyping by sequencing (GBS) using different sequencing platforms is also being tested to provide high-resolution genome scans for association mapping, introgression tracking and genomic selection.  However, more work is needed to refine the informatics tools required for analysis of large GBS data sets and user-friendly integration with additional genotype and phenotype data to facilitate a new era of precision breeding.