2006 Annual Report 4d.Progress report. This report serves to document research conducted under a specific cooperative agreement between ARS and the Department of Agronomy, University of Nebraska, and is a subcontract derived from a grant from the United Soybean Board (Grant #5212) and supports the objectives of parent project 1275-21000-164-00D. Additional details of the research can be found in the report for the parent project 1275-21000-164-00D (A Single Nucleotide Polymorphism-based Map of Soybean and Applications to Gene Discovery in Germplasm). The objective of this agreement is the genetic mapping of new SNP DNA markers. The SNP markers are first discovered at the USDA, ARS, Beltsville. Assays to permit the high throughput analysis of newly discovered SNP markers are then developed for use on the Luminex flow cytometer at the USDA, Beltsville. The assay reagents necessary for analysis of the SNP markers on the Luminex Flow Cytometer are then forwarded to the Univ. of Nebraska. The Univ. of Nebraska lab has the DNA of three soybean recombinant inbred line (RIL) mapping populations including the Minsoy x Noir 1 and the Minsoy x Archer University of Utah mapping populations as well as the Evans x PI 209332 RIL mapping population. During the reporting period Univ. of Nebraska lab mapped 171 new SNP markers in the Evans x PI 209332 RIL population. The Univ. of Nebraska combined these mapping data with a total of 450 SNP DNA markers that were mapped in the Minsoy x Noir 1 RIL population and 154 SNPs that were mapped in the Minsoy x Archer mapping population and finalized the data for analysis at the Univ. of Utah. These are a portion of the data that allowed the first estimate of the “gene space” of the soybean genome.