2007 Annual Report 1a.Objectives (from AD-416) The objectives of this research are to develop and employ an overgo (OVERlapping oliGOnucleotides) hybridization system for the identification of soybean bacterial artificial chromosome (BAC) clones that contain specific DNA sequences. The DNA sequences to be used in the design of the overgo hybridization probes will be derived from DNA markers that have been positioned on the genetic map of soybean or that will be positioned in the near future. 1b.Approach (from AD-416) The DNA sequence of clones that contain simple sequence repeat (SSR) motifs from which SSR markers were developed and mapped on the soybean genetic map will be supplied to the Purdue University collaborator. In addition, the GenBank accessions of soybean genes in which single nucleotide polymorphism (SNP) DNA markers were discovered will be supplied to the Purdue University collaborator. These sequences will be analyzed and overgo probes selected that meet specific requirements for the creation of robust overgo probes. Approximately 1,000 overgos will be developed and anchored to the physical map which is composed of soybean BAC clones. Overgos will be ordered in plates of 96 (8 rows x 12 columns) and will be hybridized to the BAC library in 20 row and column pools (i.e. 8 row pools + 12 column pools = 20 hybridization pools), this is a nearly 5-fold reduction in the number of hybridizations if the 96 overgos were screened individually. In addition, the 10x BAC library, consisting of 92,160 individual clones, will be screened using five high-density filters (18,432 clones/filter). Thus, in one row pool hybridization, 1,105,920 individual overgo to BAC clone comparisons will be made. All data will be made public via a website and data deposition in public databases immediately after verification. 3.Progress Report This report serves to document research conducted under a specific cooperative agreement between ARS and the Department of Agronomy, Purdue University and is a subcontract derived from a grant from the United Soybean Board (Project #4239) and supports the objectives of 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 objectives of this agreement are to develop and employ an overgo (OVERlapping oliGOnucleotides) hybridization system for the identification of soybean bacterial artificial chromosome (BAC) clones that contain specific DNA sequences. The DNA sequences to be used in the design of the overgo hybridization probes will be derived from DNA markers that have been positioned on the genetic map of soybean or that will be positioned in the near future. More than 1000 overgo hybridizations to two soybean BAC libraries were successfully completed. The BAC clones identified by the overgo probes will be important in anchoring the soybean physical map to the genetic map. The information relating to the positions of the BAC-clones identified by the overgo probes is being incorporated into a web-based analysis system called CMap which is a comparative genetic mapping tool that is part of the Generic Software Components for Model Organism Databases (GMOD). With CMap it will be possible to view the position of BAC clones and BAC-contigs on the genetic map of the soybean genome. Progress is monitored via quarterly written reports. In addition, periodic meetings with the collaborator as well as contact via e-mail are used to monitor progress.