Rice Whole-Genome SNP Arrays (Rice6K, Rice60K, Rice90K) for Genomic Research and Breeding

Single nucleotide polymorphism (SNP) arrays are useful tools for geneticists and molecular breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high density and high quality rice SNP arrays. Here we report the development of a series of whole-genome SNP arrays, Rice6K, Rice60K and Rice90K. Rice6K SNP array contains about 4,500 high-quality SNP markers selected from re-sequencing data of more than 500 rice varieties. Rice60K SNP array (also called RiceSNP50) contains about 43,000 high-quality SNP markers selected from re-sequencing data of more than 800 rice varieties. The SNP markers are evenly distributed on the 12 chromosomes of rice, and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonicagroups. Application tests showed that these arrays had high genotyping accuracy (with reproducibility >99.9%), and could be used for different objectives, e.g. rice germplasm fingerprinting, gene/QTL mapping, seed authenticity check, and genetic background selection. These arrays play an important role in both functional genomics studies and genomic breeding in rice. We provide SNP array service for researches in genomics and breeding all over the world. For more details, please contact Dr. Junhua Peng via phone +86-27-8798-6823 or email pengjunhua@sinochem.com.