High-Throughput SNP Genotyping for Crop Improvement

The Genotyping Services Laboratory (GSL) has been established at IRRI to provide rapid and cost-effective marker services for rice research and breeding programs (http://gsl.irri.org). To increase our sample throughput we have implemented the Brooks PlantTrak Hx handheld leaf punching system for rapid barcoded sampling of rice leaf tissue from the greenhouse and field. Lyophilized leaf tissue in 96-well plates then proceeds to automated DNA extraction using an LGC oKtopure system with magnetic bead-based sbeadex kits. Sample tracking, inventories, and request/workflow management will be handled by the Biotracker LIMS recently configured for GSL. Sets of 24 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 top GWAS hits and gene-based and flanking SNPs. Diversity analysis, SNP fingerprinting and QTL mapping currently use an Illumina Infinium 6K SNP chip developed at Cornell University. At the same time, genotyping by sequencing (GBS) approaches with 96 and 384 barcoded samples per sequence lane are being evaluated for high-resolution genome scans at a low cost per sample. Whole genome sequence data from the 3,000 genome project and resequenced breeding lines will also facilitate more precise imputation of GBS data. User-friendly SNP data formatting and analysis tools have also been developed on the online IRRI GSL Galaxy bioinformatics workbench. Future efforts will focus on large-scale deployment of GBS across breeding materials to enable QC genotyping, tracking of donor introgressions, and integration of genome-wide prediction into the variety development pipelines.