Technical Abstract: With the introduction of new sequencing technologies, single nucleotide polymorphisms (SNPs) are rapidly replacing simple sequence repeats (SSRs) as the DNA marker of choice for applications in plant breeding and genetics because they are more abundant, stable, amenable to automation, efficient, and increasingly cost-effective. SNPs are being used in breeding programs for marker-assisted and genomic selection, association and QTL mapping, positional cloning, haplotype and pedigree analysis, developing near-isogenic lines, pyramiding useful alleles, capturing positive transgressive variation through backcross breeding, seed purity testing and variety identification. SNPs are also extensively used to determine population substructure, understand the history of domestication, and explore the ancestry of specific alleles. Major efforts to identify SNPs in rice include sequencing the rice cultivar, Nipponbare, developing BAC end-sequence for 12 wild rice forms, and resequencing 20 diverse rice cultivars. This pool of SNPs is currently being expanded through the efforts of several rice programs world-wide, identified as the Rice SNP Consortium. Subsets of this data have been used to develop low, medium and high-resolution SNP assays for many of the aforementioned purposes utilizing 96, 384, 1,536, 44,100 and 600,000 SNP assays. Resources for designing allele specific primers based on the genotypic data are discussed and the newly developed statistical method, Alchemy, to reliably perform allele calling, is introduced. Alchemy, was developed for highly inbred species, like rice, where one of the genotypic classes, i.e. the heterozygous class, is often missing and works well even if only a few samples are processed. The limitations of resequencing data and the importance of exploring the genomic diversity in the world-wide collections of wild and cultivated rice accessions are discussed.