In our most recently published genetic map of soybean markers (cf., Song et al. 2004 TAG 109:122-128), 1849 marker loci (1015 SSRs, 709 RFLPs, 73 RAPDs, 24 classical traits, 10 isozymes, six AFLPs, and 12 others) were positioned on 20 linkage groups that span 2,524 cM of Kosambi map distance in five mapping populations. However, markers known as single nucleotide polymorphisms (i.e., SNPs) are expected to be of great value in future genomic/genetic research endeavors, especially when positioned on the existing soybean map. Our goal is to determine the map positions of about 10,000 SNP markers by 2007, using four mapping populations. About 2370 soybean genes with at least one SNP have been identified to date, of which 94% are parentally polymorphic in at least one of the four populations. We expect to have 1500 of these SNPs mapped by the end of 2005. For SNP genotyping assays, our lab uses a microbead-based single base extension (SBE) method involving a labeled terminator (i.e., biotin-streptavidin) for a presence/absence (of florescence) detection of the base (A,C,T,orG) constituting a given SNP allele. Up to 100 differentially colored microbeads can be multiplex-assayed using a flow cytometer to identify a given color-coded microbead (=SNP allele) and its biotin-streptavidin emission (=Y/N). An SBE assay of each SNP allele must be assayed to detect heterozygotes. Another method used for SNP detection involves creating an SBE product from a SNP allele that has more mass than the SBE product of the other SNP allele, then using MALTI-TOF mass spectrometry to determine if the genotype is a homozygote for SNP allele 1 or 2 (or a heterozygote). The presentation will provide insights on performing SNP genotype assays in the four mapping populations, and the use of the assay data to position these SNPs on the current soybean genetic map.