High-Throughput SNP Genotyping for Breeding Applications in Rice in the Genotyping Services Lab at IRRI

High-throughput genotyping methods using single nucleotide polymorphism (SNP) markers now provide the opportunity to mainstream marker-assisted selection into rice breeding programs. A Genotyping Services Laboratory (GSL) is being established at IRRI to provide rapid and cost-effective marker services, including an improved sample preparation workflow to increase the efficiency of rice leaf tissue sampling, DNA extraction, and DNA quality control in preparation for SNP genotyping. Fixed sets of 384 SNPs for both Indica germplasm and Indica/Japonica material are now routinely used for genetic diversity analysis, QTL mapping, and marker-assisted backcrossing.   Flexible sets of 24 and 96 SNPs on a Fluidigm EP1 system are being tested to enable fast, low-cost genotyping of target-specific markers of QTLs and genes controlling key traits, and to provide quality control tests to detect seed labeling errors.  SNP fingerprinting databases are being developed to support variety identification and diversity analysis. 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. By focusing on a central facility with the most cost-effective solutions for marker genotyping, the GSL will increase cost-savings and give faster turn-around times for rice research and breeding programs in the Global Rice Science Partnership, both for IRRI and research partners around the world.