Project Number: 1275-21000-263-17
Project Type: Specific Cooperative Agreement

Start Date: Mar 15, 2004
End Date: Mar 14, 2009

Objective:
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.

Approach:
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.