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Illumina Infinium Platform

The Illumina Infinium 6k SNP chip ( has proven to be an effective genotyping system for rice diversity analysis, QTL mapping, tracking introgressions, developing specialized genetic stocks and fingerprinting at both the Genotyping Services Lab at IRRI and at Cornell University. Over 40,000 samples were run successfully, providing genotyping data for a large number of genetics, breeding and impact assessment projects of importance to people throughout the world.

The Infinium platform detects SNP alleles by adding a fluorescence-labeled allele-specific nucleotide via single-base extension and subsequent detection of the fluorescence color.

The Illumina Infinium chips are sophisticated silicon-based array devices. If you are interested to learn about the technology that drives the gold standard Infinium genotyping arrays, watch the following video:

This beadchip was designed by the group of Susan McCouch at Cornell University and is being used for SNP fingerprinting, high-resolution mapping and genome-wide SNP scans.

Several subsets of markers from BeadXpress 384-SNP sets are also included on the Infinium. The 6K BeadChip contains about 6 000 bead types, around 5,000 of them are high quality, providing about 5K SNP data points

The improved second generation 7k chip (referred to commercially as the Cornell-IR RiceLD Array) has all of the benefits of the 6K chip , but with a larger number of high quality SNP markers, including trait-specific markers.