The Rice SNP Consortium is coordinating an effort to develop a suite of low-, medium- and high-resolution SNP detection platforms and
informatics pipelines to facilitate genetic studies, breeding applications and productive collaborations among diverse rice research groups throughout the world.
Use of custom-designed SNP assays minimizes the cost per chip for breeders and geneticists, increases the efficiency of research
because discoveries made by one group can be leveraged by others using the same SNP chips, facilitates collaboration among diverse
research groups around the world, promotes interaction between the public and the private sector and enhances opportunities for training and data sharing.
A list of commercially available SNP assays that have been developed under the umbrella of the Rice SNP Consortium can be found below.
44,000-SNP assay
1536-SNP assay
384-SNP assays
A series of low-resolution SNP assays (384- and 96-plex) have recently been developed by a collaborative effort between Cornell University and IRRI. These assays are based on single base extension (SBE) technology and can be run on Illumina’s GoldenGate and BeadExpress SNP detection platforms.
The assays and were developed using information from the SNP discovery pool provided by the OryzaSNP project (McNally et al., 2009), the OMAP project (Ammiraju et al., 2006), and SNP frequency data obtained by the Rice Diversity project (NSF #0606461) (McCouch et al., unpublished).